title: IL-12-induced immune suppressive deficit during CD8+ T-cell differentiation

city: Iowa City

first: Nitin

last: Karandikar

state: Iowa

address: C673 General Hospital

institute: University of Iowa

summary: Autoimmune diseases are characterized by regulatory deficit in both the CD4+ and CD8+ T-cell compartments. We have shown that CD8+ T-cells associated with acute relapse of multiple sclerosis are significantly deficient in their immune suppressive ability. We hypothesized that distinct CD8+ cytotoxic T-cell (Tc) lineages, determined by cytokine milieu during naïve T-cell differentiation, may harbor differential ability to suppress effector CD4+ T-cells. We differentiated purified human naïve CD8+ T-cells in vitro toward Tc0 (media control), Tc1 and Tc17 lineages. Using in vitro flow cytometric suppression assays, we observed that Tc0 and Tc17 cells had similar suppressive ability. In contrast, Tc1 cells showed significant loss of suppressive ability against ex vivo CD4+ T-cells and in vitro-differentiated Th0, Th1 and Th17 cells. Of note, Tc1 cells were also suboptimal in suppressing CD4-induced acute xenogeneic graft versus host disease (xGVHD) in vivo. Tc subtypes derived under various cytokine combinations revealed that IL-12-containing conditions resulted in less suppressive cells exhibiting dysregulated cytotoxic degranulation. RNASeq transcriptome analyses indicated differential regulation of inflammatory genes and enrichment in GM-CSF-associated pathways. These studies provide insights into the role of T-cell differentiation in CD8 suppressive biology and may reveal therapeutically targetable pathways to reverse suppressive deficit during immune-mediated disease.

overall_design: Ex vivo-purified CD8+ T-cells isolated from 2 healthy donors (Pr44 and Pr46) and sequenced after in vitro culture for 7 days under the following conditions: Tc0 - media only control; Tc1-A: anti-IL-4, 10 ng/ml IL-12, 10 ng/ml IL-2; Tc1-B: 10 ng/ml IL-12, 10 ng/ml IL-2; Tc1-C: anti-IL-4, 10 ng/ml IL-12; Tc1-D: 10 ng/ml IL-12; Tc1-E: anti-IL-4.

first: Pranav

last: Renavikar

first: Sushmita

last: Sinha

first: Ashley

last: Brate

first: Nicholas

last: Borcherding

first: Michael

last: Crawford

first: Scott

last: Steward-Tharp

middle: J


title: Neuronal activity regulates alternative exon usage

status: Public on Nov 18 2020

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

country: Germany

institute: Charite Universitätsmedizin Berlin

type: Expression profiling by high throughput sequencing

summary: Kanate was used to induce seizures in mice, and gene expression in the hippocampus was measured

overall_design: Mice were treated with kinate and total RNA was extracted from hippocampus was extracted at time points 0,1,4,8 hours. A replicate was measured at 4 hours.

first: Guido

last: Hermey


title: Transcriptomic analysis of age-associated periventricular lesions reveals dysregulation of the immune response

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

country: United Kingdom

institute: University of Sheffield

summary: Age-associated Periventricular white matter lesions (PVL), reflecting white matter injury, are a common feature of the ageing brain.  The aim of this study was to evaluate the transcriptomic profile of PVL using microarray analysis, in order to identify which pathways and/or gene expression changes may contribute to the pathogenesis of these lesions.

overall_design:
Total RNA was extracted from the laser capture micro-dissected periventricular region of 7 non-lesional controls, 4 pre-lesions and 7 periventricular lesional snap-frozen cases obtained from the Cognitive Function and Ageing Study neuropathology cohort. Gene expression was analysed by hybridisation to Affymetrix Human Genome U133 microarrays. Genes were considered differentially expressed if they showed a 1.2-fold change and p<0.05 across replicates of the WM groups. Microarray data was analysed using Transcriptome Analysis Console (TAC) software. Microarray data were validated using NanoString technology, to confirm the gene expression profiles in age-associated periventricular white matter.
Expression profiling of Human brain periventricular region by array

first: Motaz

middle: M

last: Fadul

middle: R

first: Jonathan

last: Cooper-Knock

first: Julian

last: Kurz

first: Hayder

middle: A

last: Al-Azzawi

first: Zarki

last: Ali

first: Taylor

last: Smith

first: Fiona

middle: E

last: Matthews

first: Carol

last: Brayne

first: Stephen

middle: B

last: Wharton

first: Julie

last: Simpson


title: analysis of expression profiles and differential allelic expression of third-instar larvae (L3) that survived treatment with OP insecticide.

city: São Paulo

first: Sophie

last: Tandonnet

address: Rua do Matão, 277

country: Brazil

institute: Universidade de São Paulo

summary: The emergence of insecticide resistance is a fast-paced example of the evolutionary process of natural selection. In our study, we investigated the molecular basis of resistance in the myiasis-causing fly Cochliomyia hominivorax (Diptera: Calliphoridae) to organophosphates (OP). By sequencing the RNA from surviving larvae treated with OP (resistant condition) and non-treated larvae (control condition), we identified genes displaying condition-specific polymorphisms, as well as those differentially expressed. Both analyses revealed that resistant individuals have altered expression and allele-specific expression of genes involved in proteolysis (specifically serine-endopeptidase), olfactory perception and cuticle metabolism, among others. We also confirmed that resistant individuals carry almost invariably the Trp251Ser mutation in the esterase E3 known to confer OP and Pyrethroid resistance. Interestingly, genes involved in metabolic and detoxifying processes (notably cytochrome P450s) were found under-expressed in resistant individuals. An exception to this were esterases, which were found up-regulated. These observations suggest that reduced penetration and aversion to OP contaminated food, may be important complementary strategies of resistant individuals. The specific genes and processes found are an important starting point for future functional studies. Their role in insecticide resistance merits consideration to better the current pest management strategies.

overall_design: Analysis of mRNA profiles of third-instar (L3) larvae treated and resistant to dimethyl-organophosphastes (resistant condition) and non-treated larvae (control condition). Two replicates per condition were examined.

first: Gisele

last: Cardoso

first: Pedro

last: Martins

first: Raquel

middle: D

last: Monfardini

first: Vanessa

middle: S

last: Cunha

first: Renato

last: Carvalho

first: Tatiana

middle: T

last: Torres


title: An epigenome-wide association study of Alzheimer’s disease blood highlights robust DNA hypermethylation in the HOXB6 gene.

city: Exeter

first: Katie

last: Lunnon

state: Devon

address: RILD South, Barrack Road

institute: University of Exeter

type: Methylation profiling by genome tiling array

summary: Alzheimer case-control samples originate from the EU funded AddNeuroMed Cohort, which is a large cross-European AD biomarker study relying on human blood as the source of DNA.

overall_design: Case-control design. Cases are Alzheimer's disease patients, individuals with mild cognitive impairment (MCI), or controls. The individuals with MCI can be further divided into individuals who had MCI at baseline blood extraction but progressed to AD within one year, or MCI individuals who didn't progress to AD within one year (see characteristics: disease status2). The criterion 'age<65.exclusion' indicates whether samples were taken into account after applying the exclusion criterion of individuals who are younger than 65 years of age.

first: Janou

last: Roubroeks


title: Biliary-Atresia-associated Mannosidase-1-alpha-2 gene regulates biliary and ciliary morphogenesis and laterality (zebrafish)

city: La Jolla

first: Shankar

last: Subramaniam

state: CA

address: 9500 Gilman Drive

department: Bioengineering

country: USA

institute: UCSD

summary: The effect of MAN1A2 on biliary morphogenesis, left-right patterning, and ciliogenesis was evaluated with knockdown in zebrafish and subsequent RNAseq experiment/analysis.

overall_design: Total RNA sequencing protocol was performed on pooled liver tissue from all three batches, one from controls and one from man1a2 morphant zebrafish. Each pool consisted of 100 livers from three batches of zebrafish larvae at 5 days post fertilization.

first: Juhoon

last: So

first: Mylarappa

last: Ningappa

first: Joe

last: Glessner

first: Jun

last: Min

first: Brandon

middle: W

last: Higgs

first: Dong

last: Li

first: Qing

last: Sun

first: Lori

last: Schmitt

first: Amy

middle: C

last: Biery

first: Steven

last: Dobrowolski

first: Christine

last: Trautz

first: Leah

last: Fuhrman

first: Molly

last: Schwartz

first: Nikolai

last: Klena

first: Joseph

last: Fusco

first: Krishna

last: Prasadan

first: Qi

last: Yan

first: Wei

last: Chen

first: William

last: Horne

first: Anil

last: Dhawan

first: Khalid

last: Sharif

first: Deirdre

last: Kelly

first: Robert

middle: H

last: Squires

first: George

middle: K

last: Gittes

first: Hakon

last: Hakonarson

first: Victor

last: Morell

first: Cecilia

last: Lo

first: Donghun

last: Shin

first: Rakesh

last: Sindhi


title: Methylome analyses of three glioblastoma cohorts reveal chemotherapy sensitivity markers within DDR genes [EORTC 26101 cohort]

city: Heidelberg

first: Tobias

last: Kessler

address: Im Neuenheimer Feld 280

institute: DKFZ

summary: The data contains Illumina 450k/EPIC array methylation files from 298 glioblastoma patients from the EORTC 26101 study

overall_design: FFPE tissue from 298 patients with glioblastoma was analyzed with Illumina 450k methylation arrays. Note that this dataset contains only samples with a IDH wild-type diffuse glioma classifier assignment

first: Wolfgang

last: Wick


title: Methylome analyses of three glioblastoma cohorts reveal chemotherapy sensitivity markers within DDR genes [Heidelberg cohort part 2]

summary: The data contains Illumina 450k/EPIC array methylation files from 18 patients with diffuse IDH wild-type glioma from the Heidelberg Neuro-Oncology center

overall_design: FFPE tissue from 18 patients with glioblastoma was analyzed with Illumina 450k methylation arrays. Note that this dataset contains only the samples that have not a classifier assignment to the GBM MES, GBM RTK I or GBM RTK II group (for the other samples see GSE122994)


title: Genome wide DNA binding profile of SOX3 in mouse testes

city: Adelaide

first: Dale

last: McAninch

state: SA

address: North Terrace

country: Australia

institute: The University of Adelaide

type: Genome binding/occupancy profiling by high throughput sequencing

summary: SOX3 is highly expressed in spermatogonial stem cells within the post natal mouse testes. A ChIP-Seq experiement was performed for SOX3 in postnatal day 7 testes.

overall_design: Identification of SOX3 binidng sites from independent ChIP-seq samples from 3 unique P7 mouse testes, compared with backgroup input DNA.

first: Ella

middle: P

last: Thomson

first: Paul

middle: Q

last: Thomas


title: Biliary-Atresia-associated Mannosidase-1-alpha-2 gene regulates biliary and ciliary morphogenesis and laterality (mouse)

first: Shankar

last: Subramaniam

summary: The effect of MAN1A2 on lung and liver development and ciliogenesis was evaluated with RNAseq analyses in knockout mice

overall_design: Total RNA was extracted from liver and lung samples from three Man1a2+/+ (WT) mice and three Man1a2-/- (Null) mice to generate mRNA sequencing libraries

first: Juhoon

last: So

first: Mylarappa

last: Ningappa

first: Joe

last: Glessner

first: Jun

last: Min

first: Brandon

last: Higgs

first: Dong

last: Li

first: Qing

last: Sun

first: Lori

last: Schmitt

first: Amy

last: Biery

first: Steven

last: Dobrowolski

first: Christine

last: Trautz

first: Leah

last: Fuhrman

first: Molly

last: Schwartz

first: Nikolai

last: Klena

first: Joseph

last: Fusco

first: Krishna

last: Prasadan

first: Qi

last: Yan

first: Wei

last: Chen


title: Analysis of gene expression in Sox10 Dom mutant sacral neural crest cells

status: Public on Nov 17 2020

city: Hongkong

first: Taida

last: Huang

address: 39 Area

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary:
Hirschsprung’s disease (HSCR) is a congenital disease which is characterized by the reduction or absence of neurons and glial cells in the enteric nervous system (ENS). Failure of neural crest cells (NCCs) to colonize the gut during the embryonic development has been considered as one of the possible causes of the disease.
In this study, the migration and gene expression of sacral NCCs from the spontaneous mouse mutant Dominant megacolon (Dom) which is a HSCR animal model expressing a mutated transcription factor Sox10, were analyzed in order to identify candidate genes which may possibly affect the NCC migration in the mutant.

overall_design: The gene expression of Sox10 Dom mutant and wildtype sacral neural cells were compared using Affymetrix GeneChip mouse Gene 1.0 ST Arrays.

first: Yonghui

last: HOU

last: HUANG


title: Methylome analyses of three glioblastoma cohorts reveal chemotherapy sensitivity markers within DDR genes

first: Tobias

last: Kessler

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

BACKGROUND: Gliomas evade current therapies through primary and acquired resistance and the effect of temozolomide is mainly restricted to the subgroup of methylguanin-O6-methyltransferase promoter (MGMT) hypermethylated tumors. Further resistance markers and pathways against chemotherapy and radiotherapy are largely unknown and would help for better stratification.

METHODS: The diagnostic cohorts involved clinical data and methylation profiles of the NOA-08 (n = 104, elderly glioblastoma) and the EORTC 26101 (n = 297, glioblastoma) studies and 398 patients with glioblastoma from the Heidelberg center. Twenty-eight glioblastoma CpGs from 17 DNA damage response (DDR) genes that negatively correlate with expression derived from a 450 DDR gene list as well as telomerase reverse transcriptase (TERT) promoter mutations were investigated for outcome and interaction with therapy and classifier assignments.

RESULTS: CpG methylation in IDH wildtype tumors had the highest association with the mesenchymal (MES) and receptor tyrosine kinase (RTK) I glioblastoma subgroup. MES tumors have lower tumor purity and differ in copy number variations on chromosomes 7 and 10 from the RTK I and II subtypes. CpG hypomethylation of DDR genes (TP73, CCND3, CSNK1E, EXO1, CUL4A and PRPF19) correlated with worse patient survival in particular in MGMT unmethylated tumors. TERT promoter mutation is most frequent in RTK I and II subtypes and associated with worse survival in primary glioblastoma. Primary glioma cells show methylation pattern that resemble RTK I and II glioma and differ from long term established cell lines. Knock-down of selected resistance genes PRPF19 and TERT increase sensitivity to temozolomide treatment in vitro.

CONCLUSION: Methylation of DDR genes and TERT promoter mutations are associated with tumor prognosis, dependent on the methylation cluster and MGMT promoter methylation status in high-grade glioma.

overall_design: Refer to individual Series


title: Lamin A/C regulates lncRNAs and epigenetic network in the heart

city: Houaton

first: Ali

last: Marian

state: Texas

address: 6770 Bertner Ave DAC C900a

department: Centre for Cardiovascular Genetics

institute: UTHSC, Houston

summary: Mutations in Lamin A/C (LMNA) cause a heterogeneous group of genetic disorders named as laminopathies. LMNA, an inner nuclear membrane protein, is implicated in nuclear genome organization and gene expression. Our objectives were to identify and define the coding and noncoding gene regulatory networks that are controlled by LMNA in the heart. Sequencing of cardiac transcripts from 2-week old wild-type (WT, N=9) and Lmna-/- (N=8) mice showed differential expression of 2,193 protein coding  (817 up/1,222 down) and  629 long non-coding RNAs (lncRNAs) (193 up/436 down,) in Lmna-/- as compared to WT hearts. AAV9 mediated re-introduction of WT LMNA in the Lmna-/- mouse heart was associated with expression changes of (normalization towards WT) of transcript levels of 1,862 coding genes and 607 lncRNAs. Of these 500 coding and 208 lncRNAs showed complete rescue in expression upon LMNA reintroduction. Restoration of the transcript levels was associated with improved heart function and increased survival. Analysis of rescued genes identified histone H3K4 demethylases KDM5A and KDM5B, among the most activated transcriptional regulators.   GO analysis for KDM5A targets showed enrichment of genes involved in mitochondrial function and oxidative phosphorylation whereas KDM5B targets were enriched for those involved in cell proliferation and differentiation.  Furthermore, based on the publicly available KDM5A ChIP-seq, 124 differentially expressed lncRNAs were identified as putative targets of KDM5A. Consistent with these findings KDM5A and 5B protein levels is increased in nuclear extracts from Lmna-/- heart and are partially rescued upon AAV9 treatment. Thus, the findings implicate dysregulation of KDM5 and its downstream regulatory network involved in the pathogenesis of laminopathies.

overall_design: RNA-seq from Lmna-/- and AAV9 treated Lmna-/- mice heart

first: Jordi

last: Coste Pradas

first: Gaelle

last: Auguste

first: Scot

last: Matkovich

first: Raffaella

last: Lombardi

first: Suet

middle: N

first: Tyrone

last: Garnett

first: Kyle

last: Chamberlain

first: Jalish

last: Mahmud Riyad

first: Thomas

last: Weber

first: Cristian

last: Coarfa

first: A

first: Priyatansh

last: Gurha


title: Expression profile of brazilian gastric adenocarcinoma cell lines

city: Rio de Janeiro

first: Renata

last: Binato

state: Rio de Janeiro

address: Praça Cruz Vermelha 23/ 6 andar ala C

institute: INCA

summary: The ACP02 cell line was stablished from a primary diffuse adenocarcinoma (T3N2M0) and AGP01 cell was established from ascitic fluid cells from intestinal gastric adenocarcinoma (T3N2M1). mRNA samples from  cell lines were amplified, labeled, and hybridized to the Affymetrix GeneChip Human Exon 1.0 ST array.  The chip array data analysis was performed with Partek® software (http://www.partek.com).

overall_design: We analyzed 2 cell lines from gastric adenocarcinoma using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by AffymetrixExpression Console and analysed using Partek software

first: Eliana

last: Abdelhay


title: Next Generation Sequencing of lung homogenate mRNA from 8-12 week male C57BL/6 mice following Sham, Carbon Black, Ozone, or Carbon Black-Ozone Co-exposure.

city: Morgantown

first: Quincy

middle: Alexander

last: Hathaway

state: WV

address: 1 Medical Center Road

department: Exercise Physiology

institute: West Virginia University

summary: While investigation of a single inhaled toxicant may be useful, the additive effects of toxicants interacting within the body can only be modelled through co-exposure. The purpose of this study is to understand how inhalation of carbon black and ozone alters the transcriptome, and if co-exposure incites unique, genome-wide changes in the lungs.

overall_design: C57BL/6 mice (8-12 weeks old) were exposed to carbon black (10 mg/m3) and/or ozone (2 ppm) for a duration of (3 hours) over a single exposure (Day 1) or four independent exposures (Day 4). Lungs were removed, RNA isolated, and mRNA sequencing performed using the Illumina HiSeq. Libraries were built with the TruSeq® Stranded mRNA Library Prep Kit (Illumina, San Diego, CA) and run on the HiSeq 2500 (Illumina) in 51bp paired end reads. Fastq files were mapped and quantified using the mapping-based mode of Salmon 1.1.0.

first: Salik

last: Hussain

first: John

last: Hollander


title: Arabidopsis Ethylene Response Factor 19 : 35S::ERF19

city: Taichung

first: chen

middle: wei

last: han

address: No.250 Kuo-Kuang Rd

department: Institute of Biotechnology, NCHU

country: Taiwan

institute: National Chung Hsing University Institute of Biotechnology CHY LAB

summary: To identify the genes regulated by Arabidopsis ERF19. 35S::ERF19 transgenic Arabidopsis was created, them we employ whole genome microarray expression profiling as a discovery platform to identify genes with the potential to regulae by ERF19. The RNA was isopated from the whole flower of control and 35S::ERF19 transgenic Arabidopsis.

overall_design: Arabidopsis ERF19 was expressed by 35S promoter to create transgenic Arabidopsis.

first: Chang

last: Yang

first: Pei

middle: F

last: Li


title: Is intestinal bacterial diversity enhanced by trans-species spread in the mixed-species flock of hooded crane (Grus monacha) and bean goose (Anser fabalis) wintering in the lower and middle Yangtze River floodplain?

city: Hefei

first: Yang

last: Zhuqing

address: School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China

country: China

institute: Anhui University

summary: Illumina high-throughput sequencing was used to analyse the intestinal bacteria of these two species during different wintering periods at Shengjin Lake. We tested whether contact time enhances the trans-species spread of gut bacteria. Our results indicate that although intestinal microflora of hooded crane and the bean goose were different, direct or indirect contact in the mixed-species flock caused the spread of gut bacteria trans-species, and a very high proportion of common pathogens among these two hosts.

overall_design: Studies on intestinal bacteria of two different species of hooded crane and bean goose, including 57 samples of hooded crane and 52 samples of bean goose.

first: Zhuqing

first: Lizhi

last: Zhou


title: Genetically defined syngeneic mouse models of ovarian cancer as tools for the discovery of combination immunotherapy (WGS)

city: Cambridge

first: Sonia

last: Iyer

state: MA

address: 455 Main Street

institute: Whitehead Institute

summary:
Purpose: There are three goals of this study of these analysis: 1. To compare the genomic, exome and chromatin accessiblity profiles of the specific engineered fallopian tube cells of high-grade serous tubo-ovarian cancer (HGSC) models (this study) using whole-exome-, whole-genome- and ATAC sequencing.
Methods: Genomic DNA was extracted from the cell lines mentioned below.
Conclusions: We conclude that whole-exome, whole-genome and ATAC-seq characterization would expedite genetic network analyses and permit the dissection of complex biological functions.

overall_design: Genomic profiles from specific engineered fallopian tube cells were generated by whole-exome, whole-genome and ATAC-seq sequencing.

first: Robert

last: Weinberg

first: George

last: Bell


title: E-cigarettes compromise the gut barrier, trigger inflammation

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

summary: Despite the rising popularity of e-cigarette and vaping devices, their safety continues to be questioned. Using established murine models of acute and chronic e-cigarette aerosol inhalation, murine colon transcriptomics and organoid co-culture models, here we assessed the effects of e-cigarette use on the gut barrier. Histologic and transcriptome analyses revealed that chronic, but not acute, nicotine-free e-cigarette use was associated with inflammation and reduced expression of tight junction markers, including occludin. Exposure of murine and human enteroid-derived monolayers (EDMs) to nicotine-free e-cigarette aerosols alone or in co-culture with invasive E. coli, recapitulated the key findings observed in vivo, i.e., barrier-disruption, downregulation of occludin, inflammation, and an accentuated risk of and response to bacterial infection. These data highlight an unexpected harmful effect of ecigarette use on the gut barrier and pinpoint non-nicotine chemical components as the source of harm. Considering the importance of an intact gut barrier for host fitness, and the impact of gut mucosal inflammation on a multitude of chronic diseases, these findings are broadly relevant to medicine and public health.

overall_design: Transcriptomic profile of murine colon after exposure with e-cigarette

first: Soumita

last: Das

first: Pradipta

last: Ghosh


title: Exploitable, highly context-specific astrocytes

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: To investigate the functional heterogeneity of astrocytes from a defined brain region, we designed 14 experimental manipulations including Huntington's disease models, pathological challenges, ionic and GPCR signaling alterations, and analyzed the transcriptomic profiles of striatal astrocytes. From the analyses, we have identified context-specific changes of striatal astrocytes.

overall_design: Total 48 samples from 24 adult mice were used in this data set. Astrocyte RiboTag AAV was injected into the striatum to extract RNA specifically from striatal astrocytes. We ablated dopaminergic neurons by MPTP, used an OCD mouse model (SAPAP3 knockout), and activated Gi-GPCR pathway in striatal astrocytes of R6/2 mice. After tissue homogenization, RNA was purified from (i) cleared lysate as the input sample, and (ii) astrocyte-specific ribosome-associated RNA precipitated via a hemagglutinin (HA) tag as the IP sample.

first: Xinzhu

last: Yu

first: Jun

last: Nagai

first: Joselyn

last: Soto

first: Maria

last: Marti

first: Giovanni

last: Coppola

first: Madan

middle: M

last: Babu

first: Baljit

last: Khakh


title: Genetically defined syngeneic mouse models of ovarian cancer as tools for the discovery of combination immunotherapy (Exome)

type: Genome variation profiling by high throughput sequencing

summary:
Purpose: There are three goals of this study: 1. To compare the genomic, exome and chromatin accessiblity profiles of the specific engineered fallopian tube cells of high-grade serous tubo-ovarian cancer (HGSC) models (this study) using whole-exome, whole-genome and ATAC-seq sequencing.
Methods: For whole-exome analysis,  genomic DNA was extracted from the cell lines mentioned below.
Conclusions: We conclude that whole-exome, whole-genome and ATAC-seq characterization would expedite genetic network analyses and permit the dissection of complex biological functions.

middle: A


title: Genetically defined syngeneic mouse models of ovarian cancer as tools for the discovery of combination immunotherapy [scRNA-Seq]

summary:
Purpose: One of the goals of this study is to compare the transcriptome profiles of tumors from mice inoculated with specific engineered fallopian tube cells of high-grade serous tubo-ovarian cancer (HGSC) models (this study) using scRNA sequencing
Methods: Tumors from mice inoculated with specific engineered fallopian tube cells of high-grade serous tubo-ovarian cancer (HGSC) models  were compared using scRNA sequencing.
Conclusions: We conclude that scRNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biological functions.

overall_design: Tumor mRNA profiles from mice inoculated with specific engineered fallopian tube cells were generated by scRNA sequencing.

first: Heiko

last: Horn


title: Expression data from esophageal squamous cell carcinoma patients

city: Shenzhen

first: Renling

last: Li

address: 3002 Lantian Road, Pingshan District, Shenzhen Guangdong, China

institute: Shenzhen Technology University

summary: we conducted microarray experiments of 28 stage I-III ESCC patients based on Affymetrix Gene Chip Human Genome U133 plus 2.0 Array, performed enrichment analysis of differentially expressed genes (DEGs) as well as gene set enrichment analysis of all valid genes. Moreover, we summarized the secreted protein-encoding DEGs as well as esophagus-specific DEGs, hoping to offer some hints for early diagnosis and target for more efficacious treatment for ESCC in near future.

overall_design: In total, there were 84 paired  normal tissues, paratumor tissues, and tumor tissues from 28 ESCC patients were chosen to perform microarray analysis.

first: Huiling

last: Qiu

first: Peng

first: Wenqun

last: Xing


title: Genetically defined syngeneic mouse models of ovarian cancer as tools for the discovery of combination immunotherapy (RNA-seq)

first: Sonia

last: Iyer

summary:
Purpose: One of the goals of this study is to compare the transcriptome profiles of tumors from mice inoculated with specific engineered fallopian tube cells of high-grade serous tubo-ovarian cancer (HGSC) models (this study) using next-generation sequencing (NGS)-derived RNA-seq.
Methods: Tumors from mice inoculated with specific engineered fallopian tube cells of high-grade serous tubo-ovarian cancer (HGSC) models  were compared using RNA sequencing.
Conclusions: We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biological functions.

overall_design: Tumor mRNA profiles from mice inoculated with specific engineered fallopian tube cells were generated by deep sequencing.

first: Robert

last: Weinberg

first: M

last: Inmaculada Barrasa


title: Oleic Acid Induces Tissue-Resident FOXP3 Regulatory T Cell Suppressive Functions (bulk RNA)

city: Berkeley

first: Allon

last: Wagner

address: 378 Stanley Hall

institute: UC Berkeley

summary: Comparing the transcriptomic program induced by oleic acid to that of the pro-inflammatory arachidonic acid, we find that Tregs sorted from peripheral blood and adipose of healthy donors transcriptomically resemble the oleic acid in vitro treated Tregs, whereas Tregs obtained from the adipose tissue of relapsing-remitting MS patients more closely resemble an arachidonic acid profile

overall_design: Samples were collected from nine healthy subjects for identification of free fatty acid-induced signatures. For every subject, Tregs were subject to treatment with arachidonic acid (AA), oleic acid (OA), or none (controls).

first: Saige

middle: L

last: Pompura

first: Alexandra

last: Kitz

first: Jacob

last: LaPerche

first: Nir

last: Yosef

first: Margarita

last: Dominguez-Villar

first: David

last: Hafler


title: ACVR2B antagonism preserves skeletal muscle and cardiac function in metastatic colorectal cancer

city: Indianapolis

first: Andrea

last: Bonetto

state: IN

address: 980 W. Walnut Street, R3-C522

institute: Indiana University School of Medicine

summary: Advanced colorectal cancer remains a leading cause of death worldwide and is often accompanied by the development of liver metastases, as well as cachexia, a multi-organ wasting syndrome inclusive of both skeletal and cardiac muscle. Activin receptor type 2B (ACVR2B)-mediated signaling participates in causing skeletal wasting in several disease conditions, and its inhibition restores skeletal muscle mass and prolongs survival in cancer cacehxia. Here we wanted to asses whether ACVR2B antagonism could preserve skeletal and cardiac muscle mass and function in a model of metastatic colorectal cancer.

overall_design: 8-week old NSG male mice were intrasplenically injected with HCT116 tumor cells to mimic hepatic dissemination of cancer cells, while sham-operated animals received saline. Tumor-bearing mice received weekly injections of ACVR2B/Fc, an inhibitor of ACVR2B signaling. All animals were euthanized approximately 3 weeks following experimental intervention. mRNA was isolated from heart tissue for RNA seq.

first: Joshua

middle: R

last: Huot

first: Ashok

last: Narasimhan

first: Teresa

last: Zimmers


title: Inhibition of BRD4 Partially Rescues Dilated Cardiomyopathy and Cardiac Arrhythmias in Myocyte-Specific Lamin A/C Null Mice [RNA-Seq]

first: Ali

middle: J

last: Marian

summary: Deletion of Lmna, encoding nuclear membrane protein LMNA, specifically in mouse cardiac myocytes activates BRD4 and leads to heart failure, arrhythmias, myocardial fibrosis, apoptosis, and premature death, which were partially rescued upon inhibition of BRD4.

overall_design: RNA-seq from Cardiac myocytes from 6 control  (WT) and 6 Myocyte-Specific Lamin A/C Null Mice (Myh6-cre:LmnaF/F)

first: Gaelle

last: Auguste

first: Scot

last: Matkovich

first: Cristian

last: Coarfa

first: Matthew

last: Robertson

first: Grazyna

last: Czernuszewicz

first: Raffaella

last: Lombardi

first: Priyatansh

last: Gurha


title: Genetically defined syngeneic mouse models of ovarian cancer as tools for the discovery of combination immunotherapy

first: Sonia

last: Iyer

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


title: UTX/KDM6A suppresses AP-1 and a gliogenesis program during neural differentiation of human pluripotent stem cells[ATAC-seq]

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

summary: UTX/KDM6A is known to promote open chromatin structure to facilitate gene activation.  Although UTX is important for normal and cancer development, its molecular activities in  developmental gene regulation remain unclear. Using genetic knockout of UTX in human  embryonic stem cells, we show that UTX promotes human pluripotency and suppresses neural  differentiation. In human neural stem cells (hNSCs), UTX modulates self-renewal, is required for  neuronal differentiation, and suppresses glial/astrocytic differentiation by positively and  negatively regulating its target genes. 70% of UTX-occupied regions are associated with  epigenetic modifications known to be influenced by UTX, and UTX knockout leads to significant  changes in expression of more than 50% of its target genes but epigenetic changes in less than  6% of its target genes. UTX likely affects gene expression via alternative molecular activities in  hNSCs. Our findings reveal new functions of UTX in gene regulation and cell fate decisions in  human stem cells.

overall_design: Examination of transcription factors as UTX/KDM6A binding sites in hNSC by ChIP-Seq, along with ATAC-Seq, ChIP-Seq of H3K4me3, H3K27me3 and H3K27ac in WT and UTX KO Neuronal Maturation cells. Intergrated analysis with transcriptome.

first: Brett

last: Mulvey

first: Jamy

last: C. Peng


title: Requisite chromatin remodeling for myeloid and erythroid lineage differentiation from erythromyeloid progenitors

city: St. Louis

first: Hyung Joo

last: Lee

state: MO

address: 4515 McKinley Avenue

department: Department of Genetics

institute: Washington University School of Medicine

summary: The mammalian SWI/SNF chromatin-remodeling BAF (BRG1/BRM-associated factor) complex has an essential role in developmental and pathological processes. We show that deletion of Baf155 encoding a subunit of the BAF complex in the Tie2(+) lineage (Baf155 CKO) leads to defects in yolk sac myeloid and definitive erythroid (EryD) lineage differentiation from erythromyeloid progenitors (EMPs). The chromatin of myeloid gene loci in Baf155 CKO EMPs is mostly inaccessible and enriched mainly by the ETS binding motif. BAF155 interacts with PU.1 and is recruited to PU.1 target gene loci together with p300 and KDM6a. Treatment of Baf155 CKO embryos with GSK126, an H3K27me2/3 methyltransferase EZH2 inhibitor, rescues myeloid lineage gene expression. This study uncovers indispensable BAF-mediated chromatin remodeling of myeloid gene loci at the EMP stage. Future studies exploiting epigenetics in generation and application of EMP derivatives for tissue repair, regeneration, and disease are warranted.

overall_design: Chromatin accessibility profiles of the Baf155 CKO and WT EMPs by deep sequencing, using Illumina NextSeq.

first: Jun

last: Wu

first: Xiaoyun

last: Xing

first: Ting

last: Wang

first: Kyunghee

last: Choi


title: Inhibition of BRD4 Partially Rescues Dilated Cardiomyopathy and Cardiac Arrhythmias in Myocyte-Specific Lamin A/C Null Mice [ChIP-Seq]

first: Ali

last: Marian

overall_design: ChIP-seq for BRD4 from Cardiac myocytes from 4 control  (WT) and 4 Myocyte-Specific Lamin A/C Null Mice (Myh6-cre:LmnaF/F)


title: Inhibition of BRD4 Partially Rescues Dilated Cardiomyopathy and Cardiac Arrhythmias in Myocyte-Specific Lamin A/C Null Mice

overall_design: Refer to individual Series


title: UTX/KDM6A suppresses AP-1 and a gliogenesis program during neural differentiation of human pluripotent stem cells[RNA-seq]


title: Identification of a STAT2 transcriptome in HCT116 p53 null tumor xenografts

city: Philadelphia

first: Ana

middle: Maria

last: Gamero

state: PA

address: 3440 N. Broad St.

department: Biochemistry

institute: Temple University

summary: Our previous study revealed that the transcription factor STAT2 promoted the growth of colorectal tumors, but the molecular mechanisms by which STAT2 contributes to tumor promotion are still unknown. Given that alterations in the tumor suppressor p53 gene are very common in colorectal cancer and critical in adenoma-carcinoma transition, we investigated whether STAT2 may also be implicated in disease progression when normal p53 function is disabled. We found Stat2 silencing in colon cancer cells deficient in p53 reduced the capacity of tumor cells to migrate and invade in vitro. We also determined that Stat2 silencing impaired tumor cells to metastasize to the liver. To begin to understand how STAT2 contributes to disease progression, we performed RNA-Seq analysis on colon tumor xenografts with the purpose to identify a STAT2 transcriptome. From this study, we identified a subset of STAT2 regulated genes that in future studies will confirm their role in colon carcinogenesis.

overall_design: We silenced Stat2 expression by shRNA approach in human p53 null HCT116 colorectal cancer cells. As a negative control, we used shRNA scrambled vector control. Subcutaneous tumor xenografts were generated in individual Rag1KO mice with these two cell lines. At day 21, we harvested tumors from 3 individual mice per cell line and submitted for transcriptomic profiling via RNA-Seq analysis. We compared transcriptomes between shSTAT2 and shControl tumors. Each data point represents an individual tumor (n-3).


first: Riki

last: Kawaguchi

summary: To investigate the functional heterogeneity of astrocytes from a defined brain region, we designed 12 experimental manipulations including Huntington's disease models, pathological challenges, ionic and GPCR signaling alterations, and analyzed the transcriptomic profiles of striatal astrocytes. From the analyses, we have identified context-specific changes of striatal astrocytes.

overall_design: Total 80 samples from 40 adult mice were used in this data set. Astrocyte RiboTag AAV was injected into the striatum to extract RNA specifically from striatal astrocytes. We designed several manipulations to ablate MSNs by quinolinic acid (QA), to induce neuroinflammation by lipopolysaccharide (LPS), to reduce potassium and calcium signals and to activate Gs-GPCR pathway in striatal astrocytes. After tissue homogenization, RNA was purified from (i) cleared lysate as the input sample, and (ii) astrocyte-specific ribosome-associated RNA precipitated via a hemagglutinin (HA) tag as the IP sample.

first: Xinzhu

last: Yu

last: Nagai

first: Maria

last: Marti

first: Giovanni

last: Coppola

first: Madan

last: Babu

first: Baljit

middle: S

last: Khakh


title: The KDM5A/RBP2 histone demethylase represses NOTCH signaling to sustain neuroendocrine differentiation and promote small cell lung cancer tumorigenesis

status: Public on Nov 16 2020

city: Boston

first: Matthew

last: Oser

address: 450 Brookline Avenue, Mayer 457

institute: Dana-Farber Cancer Institute

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: UTX/KDM6A suppresses AP-1 and a gliogenesis program during neural differentiation of human pluripotent stem cells

first: Beisi

last: Xu


title: A multi-level understanding of the evolutionary trade-offs in thermal adaptation

city: La Jolla

first: Ke

last: Chen

address: Bioengineering Department, 9500 Gilman Dr.

institute: UCSD

summary: The hypothesis that increased fitness within a selective environment must be accompanied by a loss of fitness in other non-selective environments leads to the notion of evolutionary tradeoffs. Experimental evolution provides an approach to test the existence of evolutionary tradeoffs, characterize their general quality, and reveal their genetic origins. To examine the underlying mechanism for a fitness trade-off, we constructed the evolutionary trajectories of Escherichia coli K-12 at increasing temperatures up to 45.3°C, and found diverging mutational histories that led to adaptive phenotypes with and without fitness trade-offs at low temperatures. We identified genetic changes in cellular respiration, iron metabolism and methionine biosynthesis that regulated gene expression to achieve thermal adaptation and determined the presence and absence of a fitness trade-off. Our results suggested that evolutionary trade-off could be generated by a regulatory protein mutation that was beneficial in the selective conditions but forced suboptimal proteome allocation under non-selective environments.

overall_design: Expression profiling data for nine thermally adapted strains at three temperatures were generated by RNA-seq, in duplicate

first: Connor

last: Olson

first: Troy

last: Sandberg

first: Ye

last: Gao

first: Sibei

first: Ying

last: Hefner


title: Oleic Acid Induces Tissue-Resident FOXP3 Regulatory T Cell Suppressive Functions (single-cell RNA)

first: Allon

last: Wagner

overall_design: Peripheral blood and adipose tissue were collected from eight healthy donors and eight multiple sclerosis (MS) patients. Two of the MS patients were untreated (> ~1.5yrs since last treatment at the time of the procedure), and the rest had previously received disease modifying treatments (DMTs) (> 6 months prior to the procedure, but off treatment at the time of the procedure). Height and weight (and therefore BMI) are self-reported. Donor group abbreviations: HC = healthy conrols, MS.NoTrt and MS.PrevTrt = MS patients, untreated or previously treated, respectively.

first: Saige

last: Pompura

first: Alexandra

last: Kitz

first: Jacob

last: LaPerche

first: Nir

last: Yosef

first: Margarita

last: Dominguez-Villar

first: David

last: Hafler


title: Oleic Acid Induces Tissue-Resident FOXP3 Regulatory T Cell Suppressive Functions


title: Expression data from skin biopsies of  Hidradenitis suppurativa patients

city: Basel

first: Lukas

middle: Walter Andreas

last: Roth

address: Postfach

country: Switzerland

institute: Novartis Institiues for Biomedical Research

summary:
To increase disease understanding and investigate cell types and pathways active in Hidradenitis suppurativa, skin was collected from patients who had surgical removal of affected skin regions. Blocks of tissue were taken from regions defined as lesional and non-lesional.
For comparison blocks of skin were also collected from healty people undergoing plastic surgery

overall_design: RNA was ectracted from several consecutive sections of OCT embedded blocks of skin. Skin was collected from surgical discard of healthy people and Hidradenitis suppurativa patients. From the patient samples lesional, per-lesional and non-lesional samples were collected and cellular infiltration controlled by histology.

first: Till

last: Roehn


title: RNA-seq transcriptonal profiling in neonatal rat ventricular myocytes under hypertrophic growth

first: Jian

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

summary: Heart failure is a leading cause of death in US. Hypertension is one of the most important risk factor of heart failure. In the presence of high blood pressure, the heart manifests hypertrophic growth to ameliorate ventricular wall stress. This once adaptive response may progress into decompensation and heart failure. The precise mechanisms governing this transition remain elusive. Here, we aimed to identify novel signaling pathways in cardiac hypertrophic growth. Primary neonatal rat ventricular myocytes (NRVMs) were isolated from 1-2 days old rats and treated with phenylephrine or IGF-1. Total RNA was isolated for RNA-seq analysis.

overall_design: Transcriptional profiling in in neonatal rat ventricular myocytes under hypertrophic growth by RNA-seq analysis.

first: Chongshan

last: Dai

first: Yuannyu

last: Zhang

first: Zhao

last: Wang


title: Evaluation of mRNA expression changes upon TRAF4 mis-expression in HT1376 and T24 bladder cancer cell lines

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

summary: TRAF4 is highly expressed in the epithelial bladder cancer cell line, HT1376 and poorly expressed in the mesenchymal cell line, T24. We evaluated the genetic changes in HT1376 upon TRAF4 knockdown using two independent shRNAs targetting TRAF4. The changes were documented with respect to the control cell line transduced with empty vector shRNA plasmid. Also, we over-expressed (myc-tagged) TRAF4 in T24 and evaluated mRNA changes with respect to cell line over-expressing empty vector with a myc-tag.

overall_design: 3 derivative cell lines of HT1376: control with empty vector (pLKO.1) and 2 shRNAs targetting TRAF4. 2 derivative cell lines of T24: control with myc-tag over-expression and TRAF4 over-expressed cell line.

first: Prasanna

middle: V

last: Iyengar

first: Peter

last: ten Dijke


title: Peripheral blood non-canonical small non-coding RNAs as novel biomarkers in lung cancer and pulmonary tuberculosis (validation cohort)

city: Reno

first: Musheng

last: Li

address: North Virginia Street

institute: University of Nevada, Reno

type: Non-coding RNA profiling by high throughput sequencing

summary: One unmet challenge in current lung cancer diagnosis is to accurately differentiate lung cancer patients from those with other lung diseases with similar clinical symptoms and radiological features. Previous studies have reported cases of misdiagnosis for patients with lung cancer mimicking pulmonary tuberculosis (TB) or for TB patients with multiple lung nodules mimicking lung cancer progression, which is concerning for clinical practice in TB-endemic countries/regions. Here, we develop a molecular signature composed of non-canonical small non-coding RNAs in human peripheral blood mononuclear cells (PBMCs), including tRNA-derived small RNAs (tsRNAs), rRNA-derived small RNAs (rsRNAs), and YRNA-derived small RNAs (ysRNAs). This signature consists of i) the tsRNAs derived from tRNA-Ala, tRNA-Asn, tRNA-Leu, tRNA-Lys, and tRNA-Tyr that are upregulated in the lung cancer patients relative to the healthy controls and patients with pulmonary TB, ii) the rsRNAs derived from rRNA-5S that are upregulated in the lung cancer patients but downregulated in TB patients relative to the controls, and iii) the ysRNAs originating from YRNA-RNY1 that are downregulated in the lung cancer patients but upregulated in the TB patients compared with the controls. This diagnostic signature discriminates between healthy controls, lung cancer patients, and pulmonary TB subjects with high accuracy in both the discovery and validation cohorts. We conclude that the PBMC tsRNAs, rsRNAs, and ysRNAs are informative for both screening for and discriminating between lung cancer and pulmonary TB.

overall_design: We performed small non-coding RNA sequencing for the PBMC samples collected from 35 human subjects in the validation cohort, including 12 healthy controls, 15 lung cancer patients, and 8 pulmonary TB patients.


title: Expression data from Control or TRIB3-silenced HCT-8 cells

city: Beijing

first: shuang

last: shang

address: 2# Nan Wei Street

department: Pharmacology

institute: Institute of Material Medica

summary:
To determine the critical mediator of TRIB3-enhanced Wnt/beta-catenin signaling, we examined the expression profile of genes that might regulate Wnt/beta-catenin by using mRNA microarrays.
Aberrant activation of Wnt/beta-catenin signaling pathway is a major reason for the tumorigenesis of Colon cancer. However, no specific drug targeting this pathway has been in the market. Surgery combined with cytotoxic drugs are still the major therapy methods toward colon cancer. These highlighted the need for therapeutics with alternative mechanisms of action. Here we report that the elevated TRIB3 expression associates positively with Wnt/beta-catenin signaling pathway. TRIB3 interacts with beta-catenin and TCF4 to enhance the associations between TCF4/beta-catenin target genes’ promoters, which upregulates the transcriptional activity of beta-catenin, thus to promote the CSC stemness and colon cancer tumorigenesis.

overall_design: Total RNA from HCT-8 cells expressing Control-shRNA or TRIB3-shRNA were obtained. RNA quantity and quality were measured by NanoDrop ND-1000. RNA microarrays were performed.

first: Fang

last: Hua

first: Shuang

last: Shang


title: RNA-sequencing of bulk small cell lung cancer lung tumors generating by either injecting LSL-Cas9 mice with a sgControl RPP CMV Cre adenovirus or a sgKdm5a RPP CMV Cre adenovirus

first: Matthew

last: Oser

summary: We report the RNA-sequencing results from small cell lung cancer lung tumors from lox-stop-lox Cas9 mice that were injected with sgControl RPP CMV Cre adenovirus or sgKdm5a RPP CMV Cre adenovirus. Mice were enrolled in a survival study where at their endpoint, tumors were harvested and subjected to RNA-sequencing analysis. RPP-sgRb1, sgTrp53, sgRbl2. sgControl=C0111

overall_design: Bulk RNA sequencing from small cell lung cancer lung tumors that are KDM5A mutant (sgKdm5a RPP) or KDM5A WT (sgControl RPP)

middle: G

first: William

last: Kaelin Jr


title: microRNA expression signatures for rat oscc

city: shanghai

first: xueqin

last: zhu

address: zhizaoju Road 639

department: Department of Oral and Maxillofacial-Head and Neck Oncology and Faculty of Oral and Maxillofacial Surgery

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

summary: miRNA expression profiles in SD rat HNSCC

overall_design: Total RNA was isolated from 7 tongue SCC tumors and 7 normal tissue samples using mirVanaTM RNA Isolation Kit (Applied Bio system p/n AM1556) following homogenization.

first: Tingting

first: Wantao

last: Chen


title: Mouse Olfactory Epithelium

first: Rebecca

middle: K.

last: Chance

department: Molecular and Cell Biology


title: RNA-sequencing after CRISPR knockout of KDM5A in the GLC16 small cell lung cancer cell line

summary: We report the RNA-sequencing results after CRISPR inactivation of KDM5A compared to a non-targeting sgRNA 14 days after lentiviral infection of GLC16 cells

overall_design: Examination of transcriptional changes after KDM5A knockout by CRISPR/Cas9


title: Peripheral blood non-canonical small non-coding RNAs as novel biomarkers in lung cancer and pulmonary tuberculosis (discovery cohort)

overall_design: We performed small non-coding RNA sequencing for the PBMC samples collected from 59 human subjects in the discovery cohort, including 13 healthy controls, 10 pulmonary TB patients, and 36 lung cancer patients.


title: Identification of the pharmacological effects of Chrysanthemum morifolium Ramat leaves extracts on high-fat diet induced obese mice through lipid profiling

city: Daegu

first: Ri

last: Ryu

address: 80 Daehak-ro

department: Food Science and Nutrition

country: South Korea

institute: Kyungpook National University

summary: We investigated anti-obesity mechanism of Chrysanthemum morifolium Ramat leaves extracts on high-fat diet induced obese mice using lipid profiling and RNA-seq transcriptomic profling.

overall_design: Total RNA of liver was obtained from normal diet, high-fat diet (HFD), chrysanthemum leaf ethanol extract (CLE) or luteolin added high-fat diet-fed mice and mRNA expression-associated with lipid metabolism was measured in liver.

first: Myung-Sook

last: Choi


title: Single-cell RNA-seq analysis of regulatory role of Gm4665 in spermatogenesis

first: Zhongyang

address: No.5, Dongdan Santiao, Dongcheng District

institute: School of Basic Medicine, Peking Union Medical College (PUMC)

summary:
Purpose: To understand the likely mechanisms behind the effects of candidate lncRNA knockdown, we applied single-cell RNA-seq (scRNA-seq) to decipher transcriptional alterations of affected germ cells induced by Gm4665 knockdown.
Methods: We removed somatic cells and isolated RFP+ germ cells infected with AAV9-RFP from shCtrl or Gm4665-depleted testes by FACS, before performing scRNA-seq with the Chromium system (10x Genomics). For scRNA-seq, the gene cell barcode matrix was filtered based on the number of genes detected per cell (any cells with fewer than 500 or more than 4000 genes per cell were filtered out) and the percentage of mitochondrial UMI counts (any cells with more than 10% of mitochondrial UMI counts were filtered out).
Results: We separately analyzed the differentially expressed genes (DEG) induced by Gm4665 knockdown in rST and elST populations. This demonstrated that Gm4665 knockdown resulted in increased expression of 190 genes and decreased expression of 328 genes in rST, and increased expression of 135 genes and decreased expression of 35 genes in elST.
Conclusions: Single-cell transcriptional analysis of male germ cells indicated the functional requirement of Gm4665 for multiple aspects of spermatid differentiation during spermiogenesis.

overall_design: We isolated RFP+ germ cells from 3 mice per condition, including shCtrl, Gm4665-shRNA1#, and Gm4665-shRNA2#.

first: Jiayue

last: Xu

first: Kai

first: Yanyun

last: Luo


title: UTX/KDM6A suppresses AP-1 and a gliogenesis program during neural differentiation of human pluripotent stem cells[ChIP-seq]

first: Beisi

overall_design: Examination of transcription factors as UTX/KDM6A binding sites in hNSC by ChIP-Seq, along with ATAC-Seq, ChIP-Seq of H3K4me3, H3K27me3 and H3K27ac in WT and UTX KO Neuronal Maturation cells. Intergrated analysis with transcriptome.

first: Brett

last: Mulvey

first: Jamy

last: C. Peng


title: SWR1-independent association of H2A.Z to the LINC complex promotes meiotic chromosome motion

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

summary: The H2A.Z histone variant is deposited into chromatin by the SWR1 complex affecting multiple aspects of meiosis. Here we describe a SWR1-independent localization of H2A.Z at meiotic telomeres and the centrosome. We demonstrate that H2A.Z colocalizes and interacts with Mps3, the SUN component of the LINC complex that spans the nuclear envelope and links meiotic telomeres to the cytoskeleton promoting meiotic chromosome movement. H2A.Z also interacts with the meiosis-specific Ndj1 protein that anchors telomeres to the nuclear periphery via Mps3. Telomeric localization of H2A.Z depends on Ndj1 and the N-terminal domain of Mps3. Although telomeric attachment to the nuclear envelope is maintained in the absence of H2A.Z, the distribution of Mps3 is altered. The velocity of chromosome movement during meiotic prophase I is reduced in the htz1? mutant lacking H2A.Z, but it is unaffected in swr1? cells. We reveal that H2A.Z is an additional LINC-associated factor that contributes to promote telomere-driven chromosome motion critical for error-free gametogenesis.

overall_design: ChIP-seq analysis of Htz1 in S. cerevisiae in meiosis. Each bedgraph file is the results from a paired Input and ChIP sample.

first: Jonna

last: Heldrich

first: Neem

last: Patel


title: Next Generation Sequencing Facilitates Quantitative Analysis of chromatin interaction of lncRNA Gm4665 with regulatory region of target genes in male germ cells.

first: Xu

middle: jia

last: yue

address: NO.3 Dongdan street, Beijing

institute: Peking Union Medical College

summary:
Purpose: The goals of this study are to examine the possibility that Gm4665 binds to regulatory region of target genes loci in male germ cells.
Methods: we performed the Chromatin Isolation by RNA Purification (ChIRP) assay to examine the possibility that Gm4665 binds to regulatory region of target genes. Germ cell isolated from the testis of wild-type mouse were cross-linked, lysed and sonicated, and then incubated with probesets of Gm4665.  Following hybridization of biotinylated probesets to Gm4665 transcript, Gm4665-bound chromatin was retrieved. The purified DNA fragments were sequenced using high throughput next generation sequencing (Illumina HiseqXten-PE150)
Results: Analysis of the retrieved chromatin fragments by deep sequencing (ChIRP-seq) revealed Gm4665 occupancy sites were genome wide, specifically abundant enrich in intronic regions. Additionally, nearly 30% of chromatin fragments were enriched in the promoter regions of gene loci

overall_design: Examination of chromatin interaction of lncRNA Gm4665 with regulatory region of target genes in male germ cells


title: Morphine leads to global genome changes of H3K27me3 levels in mESCs by a self-regulatory mechanism of Polycomb Repressive Complex 2 (PRC2)

city: Leioa

first: Iraia

middle: Maialen

last: Muñoa Hoyos

state: Bizkaia

address: Barriso Sarriena S/N

country: Spain

institute: Universidad del País Vasco

summary:
Environmentally induced epigenetic changes can lead to health problems or disease, but the mechanisms involved remain unclear. Morphine can pass through the placental barrier leading to abnormal embryo development. However, the mechanism by which morphine causes these effects and how the sometimes persist into the adulthood is not well known. To unravel the morphine-induced chromatin alterations involved in aberrant embryo development, we explore the role of H3K27me3/PRC2 repressive complex in gene expression and its transmission across cellular generations in response to morphine.
Using mouse embryonic stem cells as a model system, we find that chronic morphine treatment (24h) induces a global down-regulation of the histone modification H3K27me3. Conversely, ChIP-seq showed a remarkable increase in H3K27me3 levels at certain genomic sites, particularly promoters, disrupting selective target genes related to embryo development, cell cycle and metabolism. By a self-regulatory mechanism, transcription of components of the PRC2 complex responsible for H3K27me3 methylation, were consistently down-regulated by morphine, with high promoter levels of H3K27me3. Down-regulation of PRC2 components persisted for at least 48h (4 cell cycles) following morphine removal, though promoter H3K27me3 returned to control levels.
Morphine induces targeting of PRC2 complex to selected promoters, including those of PRC2 components, leading to characteristic changes in gene expression and global reduction in H3K27me3. Following morphine removal, enhanced promoter H3K227me3 levels revert to normal sooner than global H3K27me3 or transcript levels of PRC2 components. We suggest that H3K27me3 is involved in initiating morphine induced changes in gene expression but not in their maintenance.

overall_design: Examination of one histone modification and transcriptomic profile in mESCs after morphine treatment.

first: I

last: Muñoa-Hoyos

first: J

last: Halsall

first: C

last: Ward

last: Garcia

first: M

last: Araolaza

last: Urizar-Arenaza

last: Gianzo

first: P

first: B

last: Turner

first: N

last: Subiran


title: ChIP-sequencing of high grade glioma (HGG) mouse cells encoding for H3.3-G34R vs H3.3-WT histones, derived from a Sleeping beauty based-genetically engineered mouse model.

city: Ann Arbor

first: Maria

middle: Belen

last: Garcia-Fabiani

state: Michigan

address: 4574 MSRB II, 1150 West Medical Center Drive

department: Neurosurgery

institute: University of Michigan

summary: ChIP-sequencing of H3.3-G34R and H3.3-WT HGG cells was performed for several histone marks to uncover differences on histone mark deposition related to the presence of H3.3-G34R mutation, using a Sleeping beauty derived genetically engenieered mouse model.

overall_design: We assessed the binding of H3K4me1, H3K4me3, H3K27ac, H3K36me3 and H3K27me3 across the chromatin of H3.3-WT and H3.3-G34R cells from a HGG mouse model. We used three biological replicates for each group.

last: Gc Castro

middle: B

first: Tingting

last: Qin

first: Maureen

last: Sartor


title: Gene expression signatures of CD11b+ cells in mice after myocardial infarction

city: Shanghai

first: Xiangdong

last: Yang

state: China

address: 180 Fenglin Road, Xuhui District, Shanghai

institute: Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University

summary: To further search for potential gene targets which are involved in the pathological process of myocardial infarction, we have employed whole genome microarray expression profiling as a discovery platform to identify the expression of STAT6, β1-adrenergic receptors and inflammatory cytokines. The CD11b+ cells were isolated from spleen and bone marrow of mice by magnetic beads, and the experimental mice were divided into four time points (control, MI 1week, MI 2 weeks, and MI 4 weeks). We found the β1-AR related sympathetic signal, the STAT6 signal and inflammatory cytokines (IL-1α, IL-18 and TGF-β) are involved in the activation of CD11b+ immune cells and cardiac fibrogenesis after myocardial infarction.

overall_design: The gene expression was measured in spleen-derived and bone marrow-derived CD11b+ cells of mice. Mice were divided into four groups (control, MI 1week, MI 2 weeks and MI 4 weeks). There were five mice in each group.

first: Weiwei

last: Zhang


title: Genome-wide maps of chromatin state in KMT2D Knockout and KMT2D WT melanoma in mice

city: Houston

first: Mahinur

last: Mattohti

state: TX

address: 6670 Bertner Ave

department: Surgery

institute: Houston Methodist Research Institute

summary: Somatic mutations in various epigenetic regulators, including histone methyltransferases KMT2C and KMT2D, have emerged as important cancer-driving events. However, the mechanism of action and therapeutic vulnerability imparted by these mutations remain poorly understood. We identified KMT2D and 8 other epigenetic regulators as potential suppressors to melanoma initiation through an in vivo pooled epigenome-focused RNAi screen. Loss of KMT2D, which exhibits somatic mutations in human melanoma and other cancers, drastically enhanced melanoma progression in xenograft models and a BRAFV600E-driven genetically engineered mouse model of melanoma. Epigenome profiling of 6 histone marks and chromatin state alterations showed substantial reprogramming of H3K4me1- and H3K27ac-marked active enhancer states in KMT2D mutant tumors. Energy metabolic pathways such as glycolysis, OxPhos and TCA/electron transport showed high degree of deregulation which was confirmed with metabolic profiling. Pharmacological abrogation of glycolysis led to reduced proliferation and tumorigenesis preferentially in KMT2D mutant cells. Mechanistically, we find that enhancer loss at IGFBPs increases IGF signaling and downstream AKT phosphorylation that leads to upregulation of metabolic pathways rendering KMT2D mutant cells dependent on these energy metabolism pathways for their higher growth potential. Overall, we present evidence that KMT2D mutations promote tumorigenesis by reprogramming energy metabolism pathways through enhancer reprogramming.

overall_design: Examination of 6 different histone modifications in 2 cell types

first: Mayinuer

last: Maitituoheti

first: Kunal

last: Rai


title: RNA-seq of KMT2D Knockout and KMT2D WT melanoma in mice

overall_design: Triplicate total RNA profiles in 2 cell types


title: Enhancer Reprogramming Confers Dependence on Glycolysis and IGF signaling in KMT2D Mutant Melanoma

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

overall_design: Refer to individual Series


title: Bovine hepatic miRNAome profiling and differential miRNA expression analyses between beef steers with divergent feed efficiency phenotypes

city: Edmonton

first: Changxi

last: Li

state: Alberta

address: Agriculture/Forestry Centre

department: Agricultural, Food & Nutritional Science

country: Canada

institute: University of Alberta

summary:
The objectives of the current study was to profile miRNA expression in the liver tissue of beef steers and consequently identify differentially expressed miRNAs between efficient and inefficient beef steers.
Materials and Methods: In total 50 purebred Angus, 48 purebred Charolais and 158 Kinsella Composite breed steers were tested for individual feed intake using the GrowSafe system for an average period of 70 to 73 days. During the feedlot test animals were fed at ad libitum with a finishing diet composed of 75% barley grain, 20% barley silage and 5% rumensin pellet. Body weight of each animal was measured at an interval of 28days and ADG for each animal was obtained from a linear regression of serial body weight (BW) measurements (Kgs) on time (days). MWT was calculated as midpoint BW0.75, where midpoint BW was computed as the sum of initial BW of the animal and the product of its ADG multiplied by half the number test days. DMI of each animal was calculated as the average daily feed intake of the animals for the time during the feedlot test (days). The expected DMI for each animal was predicted using the regression intercept and regression coefficients of ADG and MWT on actual DMI, and RFI was computed as the difference between the standardized daily DMI and the expected DMI. At the end of the test, animals were slaughtered and liver tissue was collected immediately after slaughter separately bagged in plastic bags, labelled and flash frozen in liquid nitrogen. The frozen samples were transferred to the laboratory on ice and stored at -80C until RNA extraction. From the frozen samples, 20 samples (10 with positive and 10 with negative RFI phenotype values) of each breed were considered for total RNA extraction.  Each of the selected liver tissue sample was pulverised into fine powder using liquid nitrogen and a pre-chilled mortar and pestle on dry ice. Total RNA containing small RNAs was then extracted using a Qiagen RNeasy Plus Universal Mini Kit (Qiagen, Toronto, ON). NanoDrop 2000 Spectrophotometer (Thermo Scientific, Wilmington, DE, USA) was used to quantify the RNA. We obtained total RNA of an average concertation of 1851.8ng/µl per sample, and with absorbance ratios (A260/280) ranging between 1.8 and 2.0 which were considered of high purity for downstream analyses. RNA integrity was confirmed using a TapeStation-Agilent instrument (Agilent Technologies Canada, Mississauga, ON), RNA integrity number (RIN) values for all samples were higher than 8 which deemed them of high quality for cDNA library preparation. In total 60 cDNA libraries were prepared and sequenced at Clinical Genomics Centre (Toronto, ON, Canada). The libraries were prepared using the Illumina Truseq Small RNA Library Prep Kit (Illumina, San Diego, CA, USA) from 1µg of each of total RNA samples we submitted. Firstly, an RNA 3’ adapter was ligated to the 3’ end of the RNAs in the total RNA sample using T4 RNA Ligase 2 enzyme, thereafter an RNA 5’ adapter was added to the 5’ end of the 3’ adaptor-ligated-RNAs using T4 RNA Ligase. The RNA 3’ and RNA 5’ adapters are designed to specifically target miRNAs and other small RNAs resulting from similar biogenic processing. The 5’ and 3’ adapter ligated RNA was then Reverse transcribed using SuperScript II Reverse Transcriptase (Thermo Fisher Scientific, San Jose, CA, USA) and the RNA RT primer to generate single stranded cDNA. The cDNA was then PCR amplified a common RNA PCR primer, and a second RNA PCR primer containing a six-nucleotide indexing sequence to allow multiplexed sequencing of multiple samples on the same flow cell lane. The cDNA libraries were purified via gel electrophoresis using a 6% PAGE Gel, and the 160bp and 145bp cDNA bands were used for sequencing. Four sequencing pools of 15 samples were constructed by pooling an average of 2nM cDNA of each sample. The pooled cDNA libraries were single end sequenced on two flow cells using the Illumina Hiseq 2500 sequencing platform under Rapid run mode, with expected read length of 50bp (1x50bp SR). After sequencing raw sequence data were demultiplexed into individual FASTQ file each sample using Illumina bcl2fastq-v2.17.1.14 conversion software (Illumina). Adaptors on the 3' end of the sequences were clipped of using Cutadapt version 1.16, and consquently filtered for other small RNA species using bowtie-1.1.1 short read aligner.  Individual miRNA (including known and novel miRNAs) were profiled using the UMD3.1 bovine reference genome and the miRDeep2 package (version 2.0.0.8), Differential miRNA expression analyses within each breed was performed between six extreme low RFI and high RFI animals using edgeR package in R, at a threshold of P < 0.05 and Fold change > 1.5.
We identified 588 miRNAs as expressed in the liver tissue of the studied animals of which 90% of these miRNAs were expressed in animals from all three breed populations. Ten previously identified (known) miRNAs including bta-miR-192, bta-miR-143, bta-miR-148a, bta-miR-26a, bta-miR-30a-5p, bta-miR-22-3p, bta-miR-27b, bta-let-7f, bta-miR-27a-3p, and bta-miR-101 showed exceptionally high expression in the liver tissue of all steers, accounting for over 78% of the aligned sequence reads. We also identified 241 novel bovine miRNAs, of which the majority (69%) were uniquely expressed in one of the three breed populations. We identified 12 (7 up- and 5 down- regulated in low-RFI animals), 18 (12 up- and 6 down- regulated in low-RFI animals), and 12 (8 up- and 4 down- regulated in low-RFI animals) DE miRNAs for Angus, Charolais, and KC steers, respectively. Most of the DE miRNAs were breed specific, with only bta-miR-449a being differentially expressed in all three breeds.

overall_design: miRNA profiling of liver from three breed populations

first: Robert

last: Mukiibi

first: Dayle

last: Johnston

first: Michael

last: Vinsky

first: Carolyn

last: Fitzsimmons

first: Paul

last: Stothard

first: Sinead

last: Waters


title: A dual T-box riboswitch in Enterococcus faecium binds two tRNAs

city: Rennes

first: Vincent

last: Cattoir

address: 2 rue Henri Le Guilloux

country: France

institute: CHU de Rennes

summary: A set of small RNAs was identified in Vancomycin-resistant Enterococcus faecium, a leading cause of MDR infections. We described here the function of srn_2050, acting as a T-box riboswitch to regulate expression of downstream genes encoding the HisRS and AspRS aminoacyl-tRNA synthetases. Comparative RNAseq between Aus0004 and isogenic srn_2050 mutant identified the genes whose expression is impacted by the RNA. srn_2050 structure in its ‘off state’ was deciphered by in-line probing, containing T-box consensus sequences, a pseudoknot, a specifier loop and a terminator. Transcription binding assays between the riboswitch and either tRNAAsp or tRNAHis indicate that each deacylated tRNA interacts with the T-box. Their anticodons bind to a GACAC sequence within the specifier loop (GAC and CAC are Asp and His codons, respectively), whereas tRNATyr (UA/C-U) does not. A pioneering evaluation of E. faecium amino acid auxotrophy, with emphasis on E. faecium strain Aus0004, revealed auxotrophy for Histidine but not for Aspartic acid. Based on comparative growths and RNAseq between Aus004 and Aus004-srn2050, the riboswitch is shown essential for growth under aspartate starvation. This is the first example of a functional riboswitch in E. faecium with two overlapping codons allowing a dual tRNA-dependent regulation at transcriptional level.

overall_design: Transcriptome analysis by RNA-seq to compare the levels of all transcripts in srn2050-deleted E. faecium Aus0004 mutant versus wild-type strain and in trans-complemented srn2050-deleted E. faecium Aus0004 mutant versus srn2050-deleted E. faecium Aus0004 mutant with empty plasmid

first: Killian

last: Le Neindre

first: Freya

last: Wencker

first: Sophie

last: Reissier

first: Loren

last: Dejoies

first: Wilma

last: Ziebuhr

first: Brice

last: Felden


title: SFR KO mice germinal center B cell RNA sequencing

city: Montreal

first: André

last: Veillette

state: QC

address: 110 Des Pins Ouest Rm1065

department: Molecular Oncology

institute: IRCM

summary: WT-AID-GFP+ and SFR KO-AID-GFP+ mice were immunized with NP(18)OVA+ alum, on Day 9, germinal center B cells (AID-GFP+) were sorted for total RNA

overall_design:
Examination of wild-type vs. SFR KO germinal center B cell RNA profile

The SFR KO mice are described at: https://rupress.org/jem/article/213/10/2187/54640/Deletion-of-Slam-locus-in-mice-reveals-inhibitory
The deletion spans from the intron 1 of Cd244 to exon 8 of Slamf6:
-Cd244
-Ly9
-Slamf7
-Cd48
-Slamf1
-Cd84
-Slamf6

first: Ming-chao

last: Zhong

first: Andre


title: Entacapone treated inguinal White Adipose Tissue (iWAT) of high fat diet-induced-obesity (DIO) mouse.

first: Bao-Fa

last: Sun

address: Da-Tun Road

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


title: Broad non-coding transcription suggests genome surveillance by RNA Polymerase V

first: Shriya

last: Sethuraman

state: MI

address: 5164 Biological Sciences Building, 1105 N. University Ave.

department: Bioinformatics

summary: Eukaryotic genomes are pervasively transcribed, yet most transcribed sequences lack conservation or known biological functions. In Arabidopsis thaliana RNA polymerase V (Pol V) produces non-coding transcripts, which base-pair with small interfering RNA (siRNA) and allow specific establishment of RNA-directed DNA methylation (RdDM) on transposable elements. Here, we show that Pol V transcribes much more broadly than previously expected, including subsets of both heterochromatic and euchromatic regions. At already established RdDM targets Pol V and siRNA work together to maintain silencing. In contrast, some euchromatic sequences do not give rise to siRNA but are covered by low levels of Pol V transcription, which is needed to establish RdDM de novo if a transposon is reactivated. We propose a model where Pol V surveils the genome to make it competent to silence newly activated or integrated transposons. This indicates that pervasive transcription of non-conserved sequences may serve an essential role in maintenance of genome integrity.

overall_design: Immunoprecipitation followed by Analysis of RNA Ends (IPARE) with an anti-NRPE1 antibody was performed on 24 samples, which include 11 different genotypes (Col-0:6replicates; nrpe1:5replicates; spt5l,ago4,dms5-1,drd3-3: 2replicates each, drd1,dms3,suvh2, suvh9, suvh2/suvh9: 1replicate each)

first: Masayuki

last: Tsuzuki

first: Adriana

middle: N

last: Coke

first: M

middle: H

last: Rothi

first: Alan

middle: P

last: Boyle

first: Andrzej

middle: T

last: Wierzbicki


title: Transcriptome analysis of calcineurin-mediated genes in Fusarium oxysporum f. sp. lycopersici 4287

city: Taipei

first: YI-HSUAN

last: HOU

address: Roosevelt Rd

institute: National Taiwan University

summary: To further understand the abnormal phenotype of the calcineurin mutant strains and identify calcineurin-mediated genes in F. oxysporum f. sp. lycopersici, we performed RNA sequencing to compare the transcriptome profiles of the wild-type (WT), Δcna1(HFW1) and Δcnb1 (HFW3) mutants. By pairwise analysis, a total of 2139 genes were differentially expressed between WT and Δcna1 mutant based on the selection criteria of four-fold change in expression (Log2 fold change > 2 or < -2, P < 0.05).  Among these, 1079 genes were upregulated and 1060 genes were downregulated. Moreover, from the comparison of WT against Δcnb1 mutant, 1412 gene were being regulated, and 840 genes were upregulated while 572 genes were downregulated. To elucidate genes that were regulated by calcineurin in  F. oxysporum f. sp. lycopersici, the gene sets obtained from the pairwise analyses were compared, giving an overlap of 737 genes. Among these, 414 genes were found to be downregulated and 323 were upregulated, indicating that these genes possibly involved in the calcineurin pathway. GO functional analysis showed these transcripts were mainly involved in the oxidation-reduction process, single-organism metabolic process, transporter activity, cofactor binding, and other metabolic and biological processes.

overall_design: Total mRNA extracted from F. oxysporum f. sp. lycopersici wild-type strain, Δcna1(HFW1) and Δcnb1 (HFW3) mutants were analyzed using RNA sequencing.

first: Yi-Hsuan

last: Hou

first: Hsuan-Fu

last: Wang

first: Li-Hang

last: Hsu

first: Ying-Lien

last: Chen


title: Transcriptomics analysis of gene expression in vehicle/Entacapone treated inguinal White Adipose Tissue (iWAT) of high fat diet-induced-obesity (DIO) mouse.

summary: The DIO mouse were  treated with Vehicle/Entacapone for 3 weeks. Total RNA was isolated from White Adipose Tissue using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq 2500 (Illumina) in paired-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used.

overall_design: Examination of gene expressive levels in Vehicle/Entacapone treated inguinal White Adipose Tissue of DIO mouse.

first: Shiming

last: Peng

first: Wen

last: Xiao

first: Baofa

first: Niu

last: Huang

first: Yuigui

last: Yang


title: Next Generation Sequencing Facilitates Quantitative Analysis of the lncRNA Transcriptome in 6 Distinct Germ Cell Types During Mouse Spermatogenesis

first: Xu

last: yue

summary:
Purpose: The goals of this study are to obtain the lncRNA landscape in 6 distinct germ cell types during mouse spermatogenesis.
Methods: RNA-seq data of lncRNAs from 6 distinct cell types were generated by deep sequencing using Illumina HiSeq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. qRT-PCR validation was performed using SYBR Green assays.
Results: Using the rRNA minus strategy, we generated a total of 1100.65 Gb paired and sequence reads with a length of 150 bp. Next, we trimmed the adaptor sequence and filtered the sequence data for low-quality reads at a high stringency with an average Phred quality score less than 20, which resulted in a total of 745.67 Gb high-quality sequence reads. After filtering the reads, almost all sequence reads had a Phred quality score higher than 20, and the percentage of Ns in the reads was nearly zero. By using unique whole-genome alignment (mouse genome (mm10)), a total of 14587 mRNA genes and 6921 lncRNA genes were expressed as fragments per kilobase of exon per million reads mapped (FPKM)>0.1 in at least one sample. In addition, to obtain fingerprint lncRNAs during spermatogenesis, we first identified 2327 differentially expressed lncRNAs between every two adjacent stages. Furthermore, we identified 437 fingerprint lncRNAs that were expressed at a FPKM > 10 of its highly expressed stage.
Conclusions: Our RNA-seq dataset comprehensively dissects the dynamic expression mode of lncRNAs during mouse spermatogenesis and generated 28 relatively robust potential lncRNA candidates in spermatogenesis.

overall_design: RNA-seq data of lncRNAs from 6 distinct cell types were generated by deep sequencing, in duplicate, using Illumina HiSeq 2500.


title: Differential gene expression of Epo induced hematopoietic stem/progenitor cell erythroid differentiation with HBBP1 depletion

summary: This work shows HBBP1 is indispensable for erythropoiesis. HBBP1 was knocked down by two specific shRNAs (shHBBP1-1, shHBBP1-2) during erythroid differentiation induced from cord blood derived hematopoietic progenitor cells. After delivering shRNAs into cells, fewer mature erythroid cells in knock-down cells compared to control cells across all differentiation timings. Differential transcriptome data analysis further revealed the overall inhibition of genes promoting erythroid differentiation.

overall_design: polyA+ RNA profiles of erythroid differentiation of hematopoietic stem/progenitor cells with HBBP1 knockdown at day8, 14.

first: Yanni

last: Ma

first: Jie

last: Gao

first: Jiayue

last: Xu

first: Siqi

last: Liu

first: Lihong

last: Shi

first: Jia

last: Yu


title: YFV Capsid changes to mRNA transcriptome of Huh7 cells

status: Public on Nov 15 2020

first: Diego

last: Mourão

address: 1230 York Avenue

institute: Rockefeller University

summary: Genome-wide analysis of changes to mRNA transcript levels upon expression of YFV capsid in Huh7 cells

overall_design: Examination of Huh7 cells expressing a Tetracycline inducible HA-Flag, TFV capsid or mutant YFV Capsid constructs for 48 hours

last: Mourao

first: Thomas

last: Carroll

first: Matthew

last: Paul

first: Alexander

last: Tarakhovsky


title: Gene expression patterns in Normal Human Epidermal Melanocytes at different time points

city: Erlangen

first: Peter

last: Dietrich

address: Fahrstr. 17

institute: FAU Erlangen-Nürnberg

summary: Normal human epidermal melanocytes (NHEM, purchased from PromoCell) were culture for one (7 days) or two weeks (14 days) and subsequently, total RNA was isolated and cDNA array analysis was performed. The array was used to determine general gene expression patterns in primary melanocytes. Moreover, gene expression alterations during cell culturing (one or two weeks) can be detected. Finally, the gene expression array is used to compared gene expression paterns with melanoma cell and tissue gene expression patterns or with other primary cell lines.

overall_design: NHEM; (Normal Human Epidermal Melanocytes) were cultured for one (7d) or two (14d) weeks


title: Mechanical control of MSC adipogenesis does not require Lamin A/C

city: Boise

last: Goelzer

state: Idaho

address: 1910 University Drive

department: Materials Science and Engineering

institute: Boise State University

summary: Mesenchymal stem cells (MSC) maintain the musculoskeletal system by differentiating into multiple cell types including osteocytes and adipocytes. Mechanical signals, including strain and low intensity vibration (LIV), are important regulators of MSC differentiation. Lamin A/C is a vital nucleoskeleton protein that provides mechanical properties to the nucleus and mechanical competency to MSCs. Loss of Lamin A/C has been associated with reduced structural integrity and genomic regulation of the nucleus, but direct involvement of Lamin A/C in mechanical regulation of MSC differentiation is unknown. We investigated the effects of Lamin A/C depletion on the nucleus and regulation of adipogenesis during mechanical stimulation. Upon Lamin A/C depletion, the nucleus experienced decreased area, height, volume, and stiffness while the focal adhesion phosphorylation in response to LIV and dynamic substrate strain remained intact. Cells experiencing Lamin A/C depletion undergo slower adipogenesis than control cells indicating a loss of genomic regulation due to the depletion of Lamin A/C. Mechanical stimulation via daily LIV application induced a reduction of adiponectin protein levels in both control and Lamin A/C depleted cells. RNA-seq data indicated a large adipogenic mRNA shift in control cells while Lamin A/C depleted cells showed a blunted adipogenic mRNA profile. Treatment with LIV did not induce large trascriptome changes in ether control or Lamin A/C depleted MSCs except for lowered intereferon response, suggested that LIV effects on adipogenesis may not occur at the transcriptional level. In summary, focal adhesion activation by dynamic mechanical signals and LINC complex elements largely remain unaltered under Lamin A/C depletion. While the adipogenic commitment was dependent upon Lamin A/C, the reduction of adiponectin protein in response to LIV was independent of Lamin A/C indicating that the Lamin A/C depletion and mechanical regulation of adipogenesis may not utilize similar pathways to elicit a response in MSCs.

overall_design: Investigation of LIV mechanical forces of adiogenic differentiation during Lamin A/C depletion. Sample groups are delineated via labeling of "S" followed by a number between 1-6. Such that samples labeled with "S1" are the first sample group and "S6" is the last. The first experimental group are samples labeled with "S1" and "S2". The second experimental group are the samples labeled with "S3" and "S4". The third experimental group's samples are labeled with "S5" and "S6". Samples labeled with "AP" are treated with only adiogeneic media. Samples labeled with "APLV" have both adipogeneic media and LIV mechanical force treatment. Samples labeled with "NAL" have neither adipogenic media nor LIV mechanical force treatment.

first: Amel

last: Dudakovic

first: Andre

last: van Wijnen

first: Gunes

last: Uzer


title: Inhibiting the Mitochondrial Sulfhydryl Oxidase ALR reduces levels of Mitochondrial COX17 and induces Differentiation of AML Cells

city: Toronto

first: Aaron

last: Schimmer

state: ON

address: 610 University avenue

institute: University Health Network

summary: Inhibition of the MIA pathway of mitochindrial protein import by targeting ALR depletes mitochondrial Cox17 and induces differentiation in AML cells

overall_design: Gene expression analysis upon knock-down of ALR by two independent shRNAs

first: Danny

last: Jeyaraju


title: Expression Profile of Serum-related Exosomal miRNAs from Parathyroid Tumor

status: Public on Nov 13 2020

first: Jiacheng

last: Wang

address: Workers’ stadium south road No.8, Chao-Yang District, Beijing, China

institute: Beijing Chao-Yang Hospital

summary:
Objective: The expression pattern of exosomal miRNAs derived from parathyroid tumor is still unknown. In the present work, we aimed to examine the differences on microRNA (miRNA) expression, present in serum exosomes, by comparing parathyroid carcinoma (PC) and parathyroid adenoma (PA).
Methods: MiRNA expression profile of serum exosomes, derived from 4 PC patients and 4 PA patients, were analyzed by next-generation sequencing technology. The differential expressions of target miRNAs were further verified in both serum exosomes and tissues of PC/PA patients by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Lastly, receiver operating characteristic (ROC) curves were plotted to investigate the efficiency of target exosomal miRNAs in distinguishing PC patients from PA controls.
Results: Multiple differentially expressed miRNAs of serum exosomes were screened out by sequencing. Based on this screening, hsa-miR-146b-5p (p=0.0846), hsa-miR-27a-5p (p=0.0412), hsa-miR-93-5p (p=0.73), hsa-miR-381-3p (p=0.1239) and hsa-miR-134-5p (p=0.0694) were up-regulated in the serum exosomes of PC patients. These results were validated by qPCR, where the trend on differential miRNA expression was consistent with the sequencing results. Specifically, the expression of exosomal hsa-miR-27a-5p was able to clearly distinguish PC patients from PA controls, and related analysis indicated that the area under the ROC curve was 0.8594 (p=0.0157).
Conclusion: Here we present, for the first time, the miRNA expression profile of serum exosomes derived from PC patients. Based on this result, we presently suggest that the exosomal hsa-miR-27a-5p may serve as a putative tumor marker for preoperative identification of PC and PA subjects.

overall_design: A total of 25 PHPT patients, including 12 PC and 13 PA patients, were included in this study. 4 cases of specimens were randomly selected from the PC (2 males and 2 females) and PA (1 male and 3 females) groups for sequencing. The remaining specimens in the PC and PA groups, together with 8 NC, were utilized for verification and analysis.


title: Allergic mediator histamine confers immunotherapy resistance in cancer patients via histamine receptor 1 on macrophage

status: Public on Nov 14 2020

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

summary: How to revive anti-tumor immunity in cancer patients is an unmet challenge. Retrospective screening of common medications revealed that patients who took antihistamines during immunotherapy treatment had significantly improved survival. We further uncovered that histamine and histamine receptor H1 (HRH1) are frequently increased in tumor microenvironment to cause T-cell dysfunction. HRH1 activation in macrophages inhibits proinflammatory signaling and dysregulates fatty acid metabolism.  HRH1 also increases membrane expression of immune checkpoint V-domain Ig suppressor of T-cell activation (VISTA) in macrophages, which renders CD8+ T-cells dysfunctional. Knockout HRH1 or antihistamine treatment negated the immunosuppressive activity of the macrophages, revitalized T-cell cytotoxic function, and restored immunotherapy response. Both animal and human data showed that allergy facilitated tumor growth and induced immunotherapy resistance via histamine/HRH1 axis, underscoring the tumor-p  rone activity of allergy. These findings demonstrate that pre-existing allergy in cancer patients can dampen response to immunotherapies and warrant perspective investigation of antihistamines as an adjuvant agent for combinatorial immunotherapy.

overall_design: We analyzed global gene expression profile of naïve macrophages derived from bone marrow of wild type C57BL/6 mice, tumor conditioned macrophages from wild type C57BL/6 mice and HRH1-/- C57BL/6 mice.


title: m6A peaks in vehicle/entacapone (ENT)-treated inguinal White Adipose Tissue (iWAT) of DIO mouse.

first: Bao-Fa

last: Sun

summary: RNA was isolated from Vehicle/Entacapone(ENT) treated mouse inguinal White Adipose Tissue using the TRIzol (Invitrogen) reagent by following the company manual. mRNA was isolated by using Dynabeads mRNA Purification Kit (Invitrogen). For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100.  Approximately 5 µg of mRNA was used for m6A-IP. The immunoprecipitated m6A modified mRNAs were then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq 2500(Illumina) in paired-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used.

overall_design: Examination of m6A peaks in Vehicle/Entacapone treated inguinal White Adipose Tissue of DIO mouse.

first: Shiming

last: Peng

first: Wen

last: Xiao

first: Baofa

first: Niu

last: Huang

first: Yuigui

last: Yang


title: Chromatin accessibility analysis of Huh7 cells upon YFV capsid expression

first: Diego

last: Mourão

summary: ATACseq analysis of chromatin accessibility  in Huh7 cells upon YFV capsid expression

last: Mourao

first: Leticia

last: Carneiro

first: Thomas

last: Carroll


title: Intranasal therapy with miRNA-219 reduces viral load and encephalomyelitis in the TMEV model of multiple sclerosis

city: Chicago

first: Ana

middle: Lis

last: Moyano

state: IL

address: 808 South Wood Street

department: Anatomy and Cell Biology

institute: University of Illinois at Chicago

summary:
Purpose: RNA sequencing of spinal cord following intranasal administration of miRNA-219 in Theiler’s murine encephalomyelitis virus (TMEV) model of multiple sclerosis
Methods: RNA isolated from spinal cords was analyzed by Next-Generation RNA Sequencing (Illumina)
Results: Here, we analyzed the therapeutic effects of miR-219 in a virus-induced demyelinating model.  Following intranasal administration of miR-219 in TMEV-infected mice, we found significant reduction of clinical signs, virus persistence (virus genome copy numbers), neuroglia activation, proinflammatory cytokine levels, and demyelination.  RNA sequencing of expressed host genes demonstrated that miR-219 potentiates transcriptional changes in cholesterol-related genes, leading to reduced levels of this lipid.
Conclusions: Since virus replication relies on hijacking cholesterol biosynthesis and trafficking of host cell endogenous pools as well as remodeling intracellular membranes, i.e., the virus replication organelles or viroplasm, treatment with miR-219 may interfere with virus RNA replication through downregulation of cholesterol synthesis.  Our findings show that miR-219 administration lessens pathological changes by reducing the CNS virus loads and favoring myelin repair.

overall_design: RNA isolated from spinal cords of TMEV-infecetd mice. Experimental groups consist of healthy mice (control) and mice with chronic demyelination treated with vehicle (TMEV+veh), scrambled miR (TMEV+miR-scr) or miR-219 (TMEV+miR-219)

first: Ernesto

last: Bongarzone

middle: L


title: Dhx9 controls effector CD8 T cell differetiation program

city: Xi’an

first: Anjun

last: Jiao

state: Shaanxi

address: No. 28, Xianning West Road, Xi'an City, Shaanxi Province

institute: Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University

summary: We provide differentially gene expression between wt and Dhx9-/- CD8 T cells from LCMV infected mice.

overall_design: Examination of gene transcription in wt and Dhx9 deficient CD8 T cells from the spleens 8 days post infection.

first: Baojun

last: Zhang

first: Haiyan

last: Liu

first: Xin


title: Composition of the whole transcriptome in the human plasma: Cellular source and modification by aging

city: Tampere

first: Arttu

last: Autio

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: Plasma contains several bioactive molecules (RNA, DNA, proteins, lipids, and metabolites), which are well preserved in extracellular vesicles, that are involved in many types of cell-to-cell interactions, and are capable of modifying biological processes in recipient cells. To obtain information about the source of mRNA molecules present in the plasma, we analyzed the plasma extracellular RNA (exRNA) of healthy individuals using RNA-sequencing and compared it to that of the peripheral blood mononuclear cell (PBMCs) of the same individual. The resultant data indicates that large proportion of the transcripts in plasma are derived from cell types other than PBMCs. To assess aging-associated changes in the plasma exRNA composition, gene ontology enrichment analysis was performed, revealing a functional decline in biological processes as a result of aging. Additionally, plasma RNA levels were analyzed with differential expression analysis, revealing 10 transcripts with significant aging-associated changes. Thus, it seems that the plasma exRNA is not fully derived from the PBMCs. Instead, other cell types supply RNAs to constitute the plasma exRNA compartment. This was true in both the young and elderly individuals that were tested. Furthermore, the RNA content of the plasma showed significant changes due to aging, affecting important biological processes.

overall_design: Seven plasma samples from healthy nonagenarians, aged 94, all female. Seven plasma samples from healthy young laboratory personnel, aged 26 to 32 median age 28, all female. The samples were RNA sequenced. Gene expression was quantified and studied.

first: Tapio

last: Nevalainen

first: Maija

last: Puhka

first: Marja

last: Jylhä

first: Mikko

last: Hurme


title: Transcriptome analysis of Sulfolobus acidocaldarius DSM 639 under sugar-free and sugar-rich conditions

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

institute: Pusan National University

summary: Sulfolobus acidocaldarius is an obligate aerobe that grows in hot and acidic environments. S. acidocaldarius have been reported to grow on a variety of organic compounds as carbon and energy sources. However, little is known about systemic elucidation of carbon utilization for biomass formation and energy metabolism in S. acidocaldarius. In this analysis, the effect of glucose on genome-wide transcriptional profiling in S. acidocaldarius DSM 639 was investigated by RNA-Seq technology.

overall_design: 2 samples examined: Cultures of Sulfolobus acidocaldarius DSM 639 under sugar-free and sugar-rich conditions

first: Jaeho

last: Cha

first: Young-Su

last: Seo


title: Regional transcriptomics of a human left atrium and implications for atrial fibrillation

city: Cleveland

first: John

last: Barnard

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic Foundation

summary: Regional differential expression of atrial fibrillation risk genes in the left atrium and pulmonary veins is not well studied, but may yield insights into atrial fibrillation pathogenesis. We tested the hypothesis that there is significant regional differential expression in left atrium structures. RNAseq was performed in 25 regions within the pulmonary veins (n=12), left atrial body (n=10), and left atrial appendage (n=3) from a 75 year old male with hypertension and atrial fibrillation who died of a stroke.  These data show that genes involved in atrial fibrillation pathogenesis have substantial regional expression heterogeneity, particularly when comparing the left atrial body, pulmonary veins and left atrial appendage.

overall_design: RNAseq was performed in 25 regions from the left atria of a single male patient.

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