title: Illumina SNP array data for Brugdata syndrome patients in Taiwan

city: Taipei

first: Tzu-Pin

last: Lu

address: No. 1, Sec. 4, Roosevelt Road

department: Department of Public Health, Institute of Epidemiology and Preventive Medicine

country: Taiwan

institute: National Taiwan University, Taiwan

summary:
Background
Brugada syndrome (BrS) is a rare inherited disease causing sudden cardiac death (SCD). Copy number variants (CNVs) can contribute to disease susceptibility, but their role in Brugada syndrome (BrS) is unknown. We aimed to identify a CNV associated with BrS and elucidated its clinical implications.

Methods
We enrolled 335 unrelated BrS patients from 2000 to 2018 in the Taiwanese population. Microarray and exome sequencing were used for discovery phase whereas Sanger sequencing was used for the validation phase. HEK cells and zebrafish were used to characterize the function of the CNV variant.

Findings
A copy number deletion of GSTM3 (chr1:109737011-109737301, hg38) containing the eighth exon and the transcription stop codon was observed in 23.9% of BrS patients versus 0.8% of 15,829 controls in Taiwan Biobank (P < 0.001), and 0% in gnomAD. Co-segregation analysis showed that the co-segregation rate was 20%. Patch clamp experiments showed that in an oxidative stress environment, GSTM3 down-regulation leads to a significant decrease of cardiac sodium channel current amplitude. Ventricular arrhythmia incidence was significantly greater in gstm3 knockout zebrafish at baseline and after flecainide, but was reduced after quinidine, consistent with clinical observations. BrS patients carrying the GSTM3 deletion had higher rates of sudden cardiac arrest and syncope compared to those without (OR: 3.18 (1.77–5.74), P<0.001; OR: 1.76 (1.02–3.05), P = 0.04, respectively).

Interpretation
This GSTM3 deletion is frequently observed in BrS patients and is associated with reduced INa, pointing to this as a novel potential genetic modifier/risk predictor for the development of the electrocardiographic and arrhythmic manifestations of BrS.

overall_design: We consecutively recruited 335 unrelated patients with BrS from 2000 to 2018 in the Taiwanese population in Taiwan; 76 were identified via symptoms of sudden cardiac arrest (SCA) or syncope early in the study period (2000–2010) and 259 more, both symptomatic and asymptomatic, were identified later (2011–2018), after the SADS-TW BrS registry increased awareness of BrS. borigines were excluded from this study. BrS was diagnosed by 2 independent cardiologists using established criteria (Shanghai BrS Score ≥ 3.5). Peripheral blood samples were collected from all participants.Omni1-Quad BeadChip microarrays (Illumina, USA) were performed according to the manufacturer's instructions.

first: Jimmy

last: Juang


title: Effects of endotoxin abundance in house dust mite on the molecular phenotype of inflammation and tissue response in mouse lung

status: Public on Jul 15 2020

city: Winnipeg

first: Christopher

last: Pascoe

state: MB

address: 602-715 McDermot Avenue, Children's Hospital Research Institute of Manitoba

department: Physiology & Pathophysiology

country: Canada

institute: University of Manitoba

type: Expression profiling by high throughput sequencing

summary: We report that the abundance of endotoxin in commercially available house dust mite extracts significantly alters the lung transcriptome and secretome in a mouse model of allergic asthma. Studies using the HDM model of asthma in mice should consider reporting the abundance of endotoxin in their commercial HDM stocks in an effort to standardize the protocols and to facilitate consistant and reliable comparison between different studies.

overall_design: 3 groups of mice challenged with either house dust mite containing high levels of endotoxin, house dust mite containing low levels of endotoxin, or control mice.

middle: D

first: Aruni

last: Jha

first: Sujata

last: Basu

first: Thomas

middle: H

last: Mahood

first: Amy

last: Lee

first: Sam

last: Hinshaw

first: Reza

last: Falsafi

first: Robert

middle: E

last: Hancock

first: Neeloffer

last: Mookherjee

first: Andrew

middle: J

last: Halayko


title: Genomic data from 48 Asian gastric patient-derived xenograft (PDX) models, 7 Asian gastric patient tumors and the 8 corresponding normal tissues

city: Freiburg

first: Vincent

last: Vuaroqueaux

address: Am Flughafen 14

department: Bioinformatics

country: Germany

institute: 4HF Biotec

summary: There is a strong need to develop patient-derived xenograft (PDX) tumor models for studying new treatment options for gastric cancer (GC). With low engraftment success, few collections of GC PDX have been reported and molecular basis of the model establishment remain largely unknown.   Here we established n=27 PDX models from n=100 GC tumors and compared their characteristics to GC patient tumors based on the recent work done by ACRG and TCGA, to evaluate the representativeness and relevance of the collection for drug testing.   We show that MSI, CIN and MSS/TP53- tumors were preferentially established as PDX, while MSS/EMT and EBV not and that PDX models retained histology and molecular subtypes of parental tumors. By using synapse database, we identified 48 druggable alterations that could be investigated with the collection. Counting alterations for these 48 genes in PDX compared to TCGA tumors revealed models frequently classified with heavily altered tumors but well preserved genomic alteration patterns specific of each GC subtype.  The molecular analysis of n=8/27 tumors and corresponding PDX at passage P1, P2 and P3 revealed variations in somatic alteration content both at single nucleotide and chromosomal level in highly unstable MSI and CIN tumors, with changes occurring mainly at P1. In two cases, we show likely emergence of rare subclones carrying known oncogenic alterations in KRAS and PIK3CA.   Significance. This study presents a resource of fully annotated GC PDX models for anticancer agent testing. We show that beside close resemblance of PDX with parental tumors, not all subtypes are established, and that the clonal selection plays a key role the establishment of certain tumors. This may have a bearing on translation of observations into the clinic and underline the need to frequently survey the molecular characteristics of the PDX models.

overall_design: total DNA samples were extracted from one or two tumor samples per patient-derived xenograft model, one piece of normal patient tissue or one piece of patient tumor using a phenol:chloroform method. After standard quality controls DNA were subjected to Affymetrix GenomeWideSNP_6 microarray hybridization.

first: Anne-Lise

last: Peille

first: Swee-Seong

last: Wong

first: Jason

last: Ting

first: Kerstin

last: Klinger

first: Bruno

last: Zeitouni

first: Manuel

last: Landesfeind

first: Woo

last: Kim

first: Hyuk-Joon

first: Seong-Ho

last: Kong

first: Isabella

last: Wulur

first: Steven

last: Bray

first: Peter

last: Bronsert

first: Nina

last: Zanella

first: Greg

last: Donoho

first: Han-Kwang

last: Yang

first: Heinz-Herbert

last: Fiebig

first: Christoph

last: Reinhard

first: Amit

last: Aggarwal


title: The pathognomonic FOXL2 C134W mutation alters DNA binding specificity

city: Vancouver

first: Martin

last: Hirst

state: British Columbia

address: 2125 East Mall

department: Microbiology and Immunology

institute: University of British Columbia

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The somatic missense point mutation c.402C>G (p.C134W) in the FOXL2 transcription factor is pathognomonic for adult-type granulosa cell tumours (AGCT) and a diagnostic marker for this tumour type. However, the molecular consequences of this mutation and its contribution to the mechanisms of AGCT pathogenesis remain unclear. To explore the mechanisms driving FOXL2C134W pathogenicity we engineered V5-FOXL2 and V5-FOXL2C134W doxycycline inducible isogenic cell lines and performed ChIP-seq and transcriptome profiling following transgenic induction. Interestingly we found that FOXL2C134W associates with the majority of FOXL2 binding sites as well as a large collection of novel regions throughout the genome. De novo motif analysis of the DNA elements uniquely bound by FOXL2C134W revealed a novel DNA motif that was not seen in the shared or FOXL2 specific DNA elements and we validated an altered DNA binding specificity for FOXL2C134W using in vitro band shift assays. Integrated analysis of FOXL2C134W specific proximal promoter binding sites and differential gene expression identified direct targets of FOXL2C134W. We validated one such target and demonstrated a FOXL2C134W dependent sensitivity to a therapeutic that targets survivin (YM155). Taken together our results suggest that FOXL2C134W pathogenicity in AGCT is driven in part by an alteration in DNA binding specificity contributing to an oncogenic transcriptional program.

overall_design: Examination of wildtype and mutant FOXL2 DNA binding, gene expression and epigenetic profiling (H3K4me1, H3K4me3, H3K27me3, H3K27ac) in SVOG3e inducible cell lines using massively parallel sequencing-based assays.

first: Annaïck

last: Carles

first: Genny

last: Trigo-Gonzalez

first: Rachelle

last: Cao

first: S-W

middle: G

last: Cheng

first: Michelle

last: Moksa

first: Misha

last: Bilenky

first: David

last: Huntsman

first: Gregg

middle: B

last: Morin


title: Expression data from "A patient-derived cell atlas of glioblastoma informs precision targeting of the proteasome" (Johansson et al, Cell Reports, 2020)

status: Public on Jul 14 2020

city: Uppsala

first: Sven

last: Nelander

address: Rudbecklab

country: Sweden

institute: Uppsala Universitet

summary:
We analysed gene expression levels in a panel of pharmacologically patient derived glioblastoma cell lines.
The purpose of the experiment was to provide gene expression data for predictive modeling of drug responses. For more information about the Human Glioma Cell Culture (HGCC) resource, see portal.hgcc.se.

overall_design: Total RNA extracted from GC lines using the RNeasy Mini kit (Qiagen) was labeled and hybridized on Affymetrix Human Transcriptome 2.0 arrays.  Expression levels were RMA-normalized employing the Affymetrix Expression Console software.

first: Patrik

last: Johansson


title: MicroRNA-mediated control of Drosophila midgut regeneration [miRNA]

city: Minneapolis

first: Hiroshi

last: Nakato

state: MN

address: 515 Delaware Street SE

department: Genetics, Cell Biology, and Development

country: USA

institute: University of Minnesota

type: Non-coding RNA profiling by high throughput sequencing

summary: The molecular mechanisms by which stem cell proliferation is precisely controlled during the course of regeneration are poorly understood. Namely, how a damaged tissue senses when to terminate the regeneration process, inactivates stem cell mitotic activity, and organizes ECM integrity remain fundamental unanswered questions. The Drosophila midgut intestinal stem cell (ISC) offers an excellent model system to study the molecular basis for stem cell inactivation. Here we show that a novel gene, CG6967 or dMOV10, is induced at the termination stage of midgut regeneration, and shows an inhibitory effect on ISC proliferation. dMOV10 encodes a putative component of the microRNA (miRNA) gene silencing complex (miRISC). Our data, along with previous studies on the mammalian MOV10, suggest that dMOV10 is not a core member of miRISC, but modulates miRISC activity as an additional component. Further analyses identified direct target mRNAs of dMOV10-containing miRISC, including Daughter against Dpp (Dad), a known inhibitor of BMP/TGF-β signaling. We show that RNAi knockdown of Dad significantly impaired ISC division during regeneration. We also identified miRNAs that are induced at the termination stage and their potential target transcripts. We propose that miRNA-mediated gene regulation contributes to the precise control of Drosophila midgut regeneration.

overall_design: Examination of the initiation and termination stages of regeneration in the Drosophila midgut

first: Masahiko

last: Takemura

first: Nanako

last: Bowden


title: MicroRNA-mediated control of Drosophila midgut regeneration [RNA]


title: MicroRNA-mediated control of Drosophila midgut regeneration [TRIBE]


title: Circular RNAs Expression in Elderly Patients with Postoperative Cognitive Dysfunction

city: Chengdu

first: Rui

last: Gao

state: Sichuan

address: No. 37 GuoXue Xiang

country: China

institute: West China Hospital, Sichuan University

summary:
Postoperative cognitive dysfunction (POCD) is one of the severe complications inducing low life quality and high mortality after surgery, especially in elderly patients.Here we probed differentially expressed circRNAs using microarray assay in POCD patients, aiming to find potential key circRNAs related to the occurrence of POCD.
Subsequently, ten dysregulated circRNAs were confirmed via quantitative real-time polymerase chain reaction (qRT-PCR) in 10 paired samples. Then, Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to probe the vital functions of dysregulated genes.

overall_design: To investigate the differentially expressed circRNAs in the serum of POCD patients and its potential role in the development of POCD, we performed circRNAs microarray to screen the differentially expressed circRNAs in serum samples from 3 patients of each of the POCD and non-POCD group. Subsequently, quantitative real-time polymerase chain reaction analysis (qRT-PCR) was utilized to verify the microarray data with the serum samples from 10 patients of each group. Cytoscape software was used to construct the circRNA-miRNA-mRNA network for circRNAs with different expression levels as well as the target genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed the biological functions of differentially expressed circRNAs target genes.

first: Chan

last: Chen

first: Tao

last: Zhu


title: Global RNA sequencing reveals enhanced photosynthetic activity and auxin response in Brassica napus treated with Pseudomonas chlororaphis PA23

first: Joey

middle: C

last: Wan

address: 50 Sifton Road

summary: Plant growth promoting bacteria (PGPB) are a growing subset of agricultural adjuncts which can be used to increase crop yield and plant productivity. Although, substantial research has been conducted on the metabolites and active molecules secreted by PGPBs; relatively little is known about their effects on the global transcriptome of the host plant. The present study was carried out to investigate changes in the gene expression landscape of early vegetative Brassica napus following treatment with Pseudomonas chlororaphis PA23. This PGPB was isolated from the soybean rhizosphere and has been extensively studied as a biocontrol agent. However, little is known about its effects on plant growth and development. Using a combination of RNA-sequencing and physiological analyses, we identified increased abundance of mRNA transcripts associated with photosynthesis and phytohormone response. Phenotypically we observed increased photosynthetic rates and larger root and shoot systems in B. napus following P. chlororaphis PA23 treatment. Lastly, we identified auxin production by P. chlororaphis PA23 which likely contributes to changes in gene expression and observed phenotypic differences in root and shoot structures. Together, the results of our study suggest that PA23 is a potent plant growth promoting agent with the potential for field applications as an agricultural adjunct.

overall_design:
Total of 8 samples:
2 time points (24hour and 7days)
2 tissue types (shoot and root)
2 replicates of each sample

first: Michael

last: Becker

first: Ayooluwa

last: Bolaji

first: Philip

last: Walker

first: Teresa

last: de Kievit

first: Dilantha

last: Fernando

first: Mark

last: Belmonte


title: Role of SIRT7 overexpression in mouse fibroblast cells NIH3T3

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: Human SIRT7 GFP or GFP alone were overexpressed in NIH3T3 cells.In confluent conditions, SIRT7GFP overexpressing cells but not GFP expressing cells showed presence of distinct compact cellular colonies composed of small sized cells (ST7). Along with this SIRT7GFP overexpressing cells with long and fibroblast morphoogy(LT7) were also present. Single cell clones from these cells were expanded to form ST7 (Small SIRT7GFP expressing) and LT7  (Long SIRT7GFP expressing)  lines. RNA from GFP expressing cells (SKGFP), ST7 and LT7 lines was then isolated and applied to microarray analysis to identify gene expression changes in two cell lines

overall_design:
RNA from GFP expressing cells (SKGFP), ST7 and LT7 lines was isolated and applied to microarray analysis to identify gene expression changes in two cell lines
Agilent Mouse Whole Genome 8x60k Microarray: AMADID: 26986

first: Shashi

last: Kiran

first: Gayatri

last: Ramakrishna


title: Arabidopsis thaliana ecotypes Rodasen-47 (Sweden) and Castelnuovo-12 (Italy) grown in high light and/or cold

city: Berkeley

first: christopher

middle: r

last: baker

state: CA

address: Koshland Hall

department: PMB

institute: UC-Berkeley

summary: Illumina HiSeq RNAseq data from the youngest fully developed leaf collected from two ecotypes of Arabidopsis thaliana, Rodasen-47 (Sweden) and Castelnuovo-12 (Italy), adapted to contrasting local climates, grown at different temperatures and/or light levels. Plants were all vegatively growing in one gallon pots to prevent root bounding. Plants were sampled at the 40th day of growth.

overall_design: Two ecotypes: Rodasen-47 (Sweden) and Castelnuovo-12 (Italy). Four growth conditions: Low light/warm, low light/cool, high light/warm, high light/cool.

first: Christopher

middle: R

last: Baker

first: Jared

last: CU-Boulder


title: Aging triggers H3K27 trimethylation hoarding in the chromatin of Nothobranchius furzeri skeletal muscle.

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

institute: Max Planck Institute for Heart and Lung Research

summary: Aging associates with progressive loss of skeletal muscle function leading up to sarcopenia, a process characterized by impaired mobility and weaken muscle strength. Sarcopenia underpinning molecular mechanisms are still poorly characterized. Since, aging associates with profound epigenetic changes, the investigation of the epigenetic landscape alteration in the skeletal muscle promises to highlight molecular mechanisms of age-associated sarcopenia. Here, the study was conducted exploiting the short-lived Nothobranchius furzeri (Nfu), a relatively new model for aging studies. The epigenetic analysis suggested for a less accessible and more condensed chromatin in old Nfu skeletal muscle. Specifically, an accumulation of heterochromatin regions was observed as consequence of increased levels of H3K27me3, HP1a, polycomb complex subunit expression and SAHFs. Consistently, euchromatin histone marks, including H3K9ac, decreased. The integrative bioinformatics analysis of RNASeq and ChIPSeq dataset, related to skeletal muscle of Nfu at different ages, revealed a down-modulation of transcripts involved in cell cycle, differentiation and DNA repair and an up-regulation of inflammation and senescence genes. Undoubtedly, more studies are needed to disclose the detailed mechanisms, but this approach shed light on unprecedented specific features of Nfu skeletal muscle aging, responsible of sarcopenia onset and consequent impairment of swimming and mobility activity typical of old Nfu.

overall_design: Skeletal muscle derived from Nothobranchius furzeri at different ages: 5 weeks, 20 weeks and 35 weeks (n=3 for each age)

first: Chiara

last: Cencioni

first: Johanna

last: Heid

first: Anna

last: Krepelova

first: Mahdi

last: Rasa

first: Stefan

last: Guenther

first: Mario

last: Baumgart

first: Alessandro

last: Cellerino

first: Francesco

last: Neri

last: Spallotta

first: Carlo

last: Gaetano


title: DNA methylation analysis of pineoblastoma

city: Memphis

first: Anthony Pak-Yin

last: Liu

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

type: Methylation profiling by genome tiling array

summary: Pineoblastoma is a rare and aggressive embryonal tumor of childhood. The molecular heterogeneity within has not been systematically evaluated. In this study, we used methylation profiling to compare the signatures of pineoblastoma and other pineal parenchymal tumors  to a reference cohort of brain tumor entities (GSE90496) , clinically relevant epigenomic subgroups with characteristics genomic/transcriptomic features are described.

overall_design: Human pineal parenhchymal tumors (n=43), including 40 pineoblastomas, were profiled using Illumina Infinium Human MethylationEpic Bead Array

first: APY

first: T

last: Lin


title: MicroRNA-mediated control of Drosophila midgut regeneration

first: Hiroshi

last: Nakato

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

overall_design: Refer to individual Series


title: Disease associated fibroblasts from various pancreatic disorders exhibit subtype specific genetic profile

city: Liverpool

first: Eithne

last: Costello

address: Ashton Street

department: Department of Molecular and Clinical Cancer Medicine

country: United Kingdom

institute: University of Liverpool

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

platform_organism:
Homo sapiens
synthetic construct


title: ATAC-sequencing of BTBR and C57BL6/J BMDM with Repeated LPS Treatment

first: Annie

middle: Vogel

last: Ciernia

address: 2215 Wesbrook Mall room 4550, Centre for Brain Health

summary: The ability of peripheral innate immune cells to control pro-inflammatory cytokines during periods of repeated or prolonged exposure to immune activating stimuli is critical for preventing tissue damage. In macrophages, repeated exposure to lipopolysaccharide (LPS) induces a refractory period of immune activation termed endotoxin tolerance. Macrophages from the BTBR mouse strain have a skewed pro-inflammatory phenotype and show a hyper-response to LPS challenge. To identify disrupted regulatory mechanisms governing control of cytokine expression in BTBR compared to C57BL/6J mice (C57), we assessed bone marrow derived macrophages (BMDM) treated with either media, one dose or two doses of LPS. Differences in chromatin accessibility using ATAC-sequencing were used to identify regions of differential chromatin accessibility both under baseline media conditions and in response to LPS.

overall_design: Bone marrow was extracted from postnatal day 28 (P28) male BTBR or C57 mice and differentiated in culture for seven days (DIV 7) to form bone marrow derived macrophages (BMDM). BMDM from each strain were re-seeded into six well plates and treated with either media, one dose of LPS for 24hrs (LPSx1) or given a 4 hour LPS pretreatment followed by a 24hour LPS treatment (LPSx2). All LPS treatments were at 100ng/ml of culture media.  Following treatment, cells were collected for ATAC-sequencing. After quality control assessment, reads were aligned to the mouse genome (mm10) and filtered for nucleosome free regions (<147bp). HOMER was then used to call peaks for each biological replicate.

middle: V

first: Janine

last: LaSalle


title: RNA-seq of Bafilomycin-treated cells

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

institute: UT Southwestern Medical Center

summary: Nonsense-mediated decay (NMD) is a pathway that degrades messenger RNAs containing premature termination codons. Here, a genome-wide screen for NMD factors uncovered an unexpected mechanism that broadly governs 3ʹ untranslated region (UTR)-directed regulation. The screen revealed that NMD requires lysosomal acidification, which allows transferrin-mediated iron uptake, which in turn is necessary for iron-sulfur (Fe-S) cluster biogenesis. This pathway converges on the Fe-S cluster-containing ribosome recycling factor ABCE1, whose impaired function results in the movement of ribosomes into 3ʹ UTRs where they displace exon junction complexes, thereby abrogating NMD. Importantly, these effects extend beyond NMD substrates, with ABCE1 activity required to maintain the accessibility of 3ʹ UTRs to diverse regulators, including microRNAs and RNA binding proteins. Due to the sensitivity of the Fe-S cluster of ABCE1 to iron availability and reactive oxygen species, these findings reveal an unanticipated vulnerability of 3ʹ UTR-directed regulation to lysosomal dysfunction, iron deficiency, and oxidative stress.

overall_design: Method: RNA-seq was performed in HCT116 NMD reporter cells that were either treated with DMSO or 5 nM bafilomycin for 48 hours. Two replicates in each condition, and thus 4 biological samples were used for these experiments.

first: Xiaoqiang

last: Zhu

first: He

last: Zhang

middle: T


title: Disease associated fibroblasts from various pancreatic disorders exhibit subtype specific genetic profile [RNA]

summary: Currently it is unknown whether activation of recruited or resident pancreatic fibroblasts, including pancreatic stellate cells activation, create a common “fibroblast-activated phenotype” indistinguishable from their associated-diseased microenvironment . Using a combination of microRNA and mRNA profiling of fibroblasts isolated from pancreatic ductal adenocarcinoma (PDAC), chronic pancreatitis (CP), periampullary cancer (PAT) and areas of histologically normal pancreas, followed by comprehensive validation, we show that activated fibroblasts derived from different pancreatic disease types are considerably distinct.

overall_design: Total RNA from primary cultures of activated fibroblasts isolated from human PDAC (n=6), CP (n=5), PAT (n=5) and adjacent normal tissue (n=5) was hybridized onto Affymetrix GeneChip Human Transcriptome 2.0 arrays.

first: Brian

last: Lane

first: Lawrence

last: Barrera


title: Evaluating developmental effects of Tmem184b in dorsal root ganglia

city: Tucson

first: Martha

last: Bhattacharya

state: AZ

address: 1040 E 4th Street

department: Neuroscience

institute: University of Arizona

summary: We evaluated transcriptomic signatures at critical timepoints of sensory differentiation in wild type and Tmem184b mutant mice.

overall_design: Wild type control C57BL/6 and Tmem184b gene-trap mutant mice (n=3-4 per timepoint and genotype) were evaluated at E13, P0, and P10

first: Erik

last: Larsen


title: Comparative transcriptional analysis of Staphylococcus epidermidis biofilm matrix variants in human platelet concentrates

city: Ottawa

first: Basit

last: Yousuf

state: ON

address: 2035, Othello Avenue, Ottawa

institute: University of Ottawa

summary: This study is focused on understanding the molecular basis of protein- and polysaccharide intercellular adhesin (PIA)- mediated biofilm formation by S. epidermidis in PCs. Comparative transcriptomic analysis of S. epidermidis PIA- biofilm positive (AZ22, AZ39) and PIA+ biofilm positive (ST02) strains was performed using a RNAseq approach. Pathway enrichment analysis revealed cellular component GO term (AZ22), two KEGG pathways (AZ39), and two molecular function GO term and 8 KEGG pathways (ST02) were enriched. Remarkably, glutamate biosynthesis and tricarboxylic acid cycle (TCA) genes were upregulated in AZ22 and AZ39, respectively whereas arginine deiminase (ADI) pathway genes were downregulated in ST02. Moreover, genes conferring resistance against antimicrobial peptides (AMPs) and antibiotics such as lysostaphin, fusidic acid and tetracycline were upregulated, thus implying their increased resistance in S. epidermidis grown in PCs. Notably, expression of genes conferring resistance against aminoglycoside (in AZ22) and methicillin (in AZ39 and ST02) were downregulated. This study  provided an overview, how biofilm-mediated virulence, antibiotic resistance and metabolic pathways are interlinked and reprogrammed during biofilm maturation in PCs which will be intriguing in development of novel preventive strategies against S. epidermidis transfusion-transmitted infections.

overall_design: Comparative transcriptomic analysis of S. epidermidis PIA- biofilm positive (AZ22, AZ39) and PIA+ biofilm positive (ST02) strain's mature biofilm formed in tryptic soya broth supplemented with 0.5% glucose (TSBg) and human platelet concentrates

first: Maria

last: Loza-Correa

first: Milos

last: Kalab

first: Sandra

last: Ramirez-Arcos


title: Alpha lipoic acid help to promote the production of hematopoietic stem/progenitor cells from human pluripotent stem cell

city: chengdu

first: Yong

last: Dong

state: sichuan

address: Xindu road 783, Xindu district

department: Immunology

institute: Chengdu medical college

summary: Hematopoietic differentiation from human pluripotent stem cell in vitro is an important approach for the research of hematopoietic stem cell regeneration. Small molecules that can maintenance low ROS level and inhibit cell apoptosis or autophagy are benifit for the maintenance or expansion of hematopoietic stem cells. Lipoic acid (ALA) as a small antioxidant molecule can regulate the ROS level and apoptosis of cells. This study found that lipoic acid promoted the production of hemogenic endothelial cells and hematopoietic progenitor cells. Transcriptome analysis of hemogenic endothelial cells showed that ALA upregulated the endothelial to hematopoietic transition (EHT) related genes and downregulated the EHT negative regulated genes. ALA also up-regulated ROS and apoptosis related genes to inhibit the apoptosis of hematopoietic stem/progenitor cells.These results indicated that ALA might have an important role in the regeneration of hematopoietic stem progenitor cell in vitro.

overall_design: To explore the molecular mechanism of ALA promoting the production of HPC derived from human pluripotent stem cells. We sorted one thousand hemogenic endothelial cells to performed RNA-seq as we described before(PMID:29434353, 31443434),

first: Feng

last: Ma

first: Ju

last: Bai


title: Time course of the miR-203 effect during reprogramming from somatic cells to pluripotent cells

city: Madrid

last: Salazar

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology

country: Spain

institute: CNIO

summary: The balance between pluripotency and differentiation is critical during development and regeneration. miR-203 is a microRNA previously involved in differentiation of different tissues as well as in tumor suppression in multiple malignancies. We have shown that miR-203 is able to promote differentiation of embryonic stem (ES) and induced pluripotent stem (iPS) cells without decreasing pluripotency. We have observed that transient expression of miR-203 significantly improves the efficiency of ES/iPS cells in the generation of quimeras and tetraploid complementation assays, in addition to inducing complex embryo-like structures when these pluripotent cells are injected in mice. In the present RNA seq, we intend to analyze the trascriptomic profile of miR-203 WT, KO and KI MEFs reprogrammed to inducible pluripotent cells (iPSCs) at different time points.

overall_design: The general idea was to analyze the transcriptomic profile of miR-203 WT, KO and KI MEFs during reprogramming to iPSCs. We collected samples at different time points: MEFs, day 0 after inducing reprogramming, day 4, day 6 and day 7 of reprogramming and finally, iPSCs generated from miR-203 WT and KO MEFs.

first: María

middle: S

last: Roa

first: Osvaldo

last: Graña

first: Marcos

last: Malumbres


title: RNA-seq of Paraquat-treated cells

first: Joshua

last: Mendell

overall_design: Method: RNA-seq was performed in HCT116 NMD reporter cells that were either treated with ddH2O or 200 μM paraquat for 96 hours. Two replicates in each condition, and thus 4 biological samples were used for these experiments.

last: Zhu


title: CRISPR screen for NMD regulators

overall_design: Method: A genome-scale CRISPR/Cas9-mediated loss of function screen for NMD regulators was performed in HCT116 cells expressing either a NMD EGFP reporter (PTC231) or control EGFP reporter (PTC35).

first: Xiaoqiang

last: Zhang


title: Ribosome profiling of ABCE1-knockout cells

overall_design: Method: Ribosome profiling was performed in HCT116 cells that received, via lentivirus, Cas9 and sgRNAs targeting either ABCE1 or non-targeting control sgRNAs. Two sgRNAs were used for each condition, and thus 4 biological samples were used for these experiments.

first: He


title: RNA-seq of ABCE1-knockout cells

overall_design: Method: RNA-seq was performed in HCT116 cells that received, via lentivirus, Cas9 and sgRNAs targeting either ABCE1 or non-targeting control sgRNAs. Two sgRNAs were used for each condition, and thus 4 biological samples were used for these experiments.


title: Ribosome recycling by ABCE1 links lysosomal function and iron homeostasis to 3ʹ UTR- directed regulation and nonsense-mediated decay


title: Genome-wide transcriptional response of Aspergillus nidulans to heterologous protein production

city: Campinas

first: Gabriela

middle: F

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

summary: Filamentous fungi are important factories in the production and secretion of homologous and heterologous lignocellulolytic enzymes, however the regulation of protein secretion in these organisms need to be further explored. In order to investigate this regulation, Aspergillus nidulans recombinant strains were analyzed by transcriptomics. We designed three A. nidulans recombinant strains producing the following heterologous proteins: alpha-arabinofuranosidase (AbfA), beta-glucosidase (BglC) and thermophilic mannanase (1542). The heterologous genes abfA and bglC were highly expressed, while the levels of 1542 mRNA were similar to the reference gene. An indirect relationship between mRNA and the levels of protein secretion was observed, suggesting that transcription is not a bottleneck in these systems. Based on the general analysis of RNA-seq of the recombinant strains, it was possible to observe a predominant up-regulation response. Moreover, biological processes related to metabolism, protein with binding function and cellular transport were overrepresented. We also observed the unconventional splicing of hacA for the recombinant A. nidulansAbfA and A. nidulans1542, indicating some level of unfolded protein response. The global analysis showed mild stress at 2 h induction of heterologous protein production, which was normalized after 8 h. Our results provide insights to understand how A. nidulans adapts to the overproduction of heterologous proteins.

overall_design: Transcriptional evaluation of three Aspergillus nidulans recombinant strains expressing heterologous proteins

first: Felipe

last: Calzado

first: Cesar

last: Terrasan

first: Mariane

middle: P

last: Zubieta

first: Marcelo

last: Rubio

first: Fabiano

last: Contesini

first: Fabio

middle: M

last: Squina

first: Andre

last: Damasio


title: Disease associated fibroblasts from various pancreatic disorders exhibit subtype specific genetic profile [miRNA]

first: Eithne

last: Costello

overall_design: Total RNA from primary cultures of activated fibroblasts isolated from human PDAC (n=6), CP (n=5), PAT (n=5) and adjacent normal tissue (n=5) was hybridized onto Affymetrix GeneChip miRNA 4.0 arrays.

first: Brian

last: Lane

first: Lawrence

last: Barrera


title: Survey functional genes in Arctic marine sediment communities

city: Tromso

first: Brandon

last: Hassett

address: Framstredet

department: Arctic and Marine Biology

country: Norway

institute: University of Tromso

summary:
The objective was to identify functional genes encoded by Fungi and fungal-like organisms to assess putative ecological roles
Using the GeoChip microarray, we detected fungal genes involved in the complete assimilation of nitrate and the degradation of lignin, as well as evidence for Partitiviridae (a mycovirus) that likely regulates fungal populations in the marine environment.  These results demonstrate the potential for fungi to degrade terrigenously-sourced molecules, such as permafrost and compete with algae for nitrate during blooms.  Ultimately, these data suggest that marine fungi could be as important in oceanic ecosystems as they are in freshwater environments.

sample_organism:
synthetic construct
marine sediment metagenome

platform_organism: Bacteria Archaea Eukaryota Viruses

overall_design: Three biological replicates were collected in both May and June sediment.  Biological replicates were pooled and DNA was subsequently extracted.  DNA was shipped to the University of Oklahoma, where it was analyzed with the GeoChip microarray

first: Joy

last: Van Nostrand


title: Transcriptomics analysis of HEK293 cells

city: Cambridge

first: Ramanujan

last: Hegde

address: Francis Crick Ave

institute: MRC Laboratory of Molecular Biology

summary: We investigate transcript levels in HEK293 cells

overall_design: One condition studied in triplicate

first: Zhewang

last: Lin


title: Maintenance of mammary epithelial phenotype by AML1/RUNX1 through mitotic gene bookmarking

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

summary: Genetic and epigenetic changes in mammary epithelial cells facilitate epithelial-to-mesenchymal transition (EMT) which leads to invasion and metastasis. RUNX1 is a phenotypic transcription factor pivotal for maintenance of mammary epithelial phenotype, whose loss leads to EMT. However, the mechanisms by which RUNX1 maintains mammary epithelial phenotype are not known. Here, we report RUNX1-mediated mitotic gene bookmarking as a key epigenetic mechanism through which RUNX1 stabilizes mammary epithelial phenotype by conveying regulatory information for cell proliferation, growth, and identity through successive cell divisions. Immunofluorescence microscopy and chromatin immunoprecipitation with high throughput sequencing of asynchronous, mitotic, and G1 MCF10A breast epithelial cells revealed RUNX1 association with target genes through interphase and mitosis. RUNX1 mitotically bookmarked both RNA Pol and II transcribed genes involved in proliferation, growth, and mammary epithelial phenotype maintenance. Inhibition of RUNX1 DNA binding by a specific small molecule inhibitor led to phenotypic changes, apoptosis, and differential expression of ribosomal RNA as well as protein coding genes (e.g. HES1 and H2AFX) and long non-coding RNA (e.g. NEAT1 and MALAT1) genes involved in cellular phenotype. Together these findings reveal a novel epigenetic regulatory role of RUNX1 in normal-like breast epithelial cells and demonstrate mitotic bookmarking target genes by RUNX1 is necessary to maintain breast epithelial phenotype. Disruption of RUNX1 bookmarking by a pharmacological inhibitor results in initiation of epithelial to mesenchymal transition, an essential first step in the onset of breast cancer.

overall_design: Investigation of RUNX1 binding sites within asynchronous, mitotic, and G1 MCF10A breast epithelial cells

first: Joshua

last: Rose

first: Joseph

last: Boyd


title: Transcriptomic profiling of circadian genes in WT mouse tissues (miRNA-Seq)

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

summary: A goal of a collaboration between the CHDI Foundation and Prof. Jenny Morton at Cambridge University was to identify genes in mice with diurnal/circadian expression patterns. Tissues from wild type mice were harvested every 3 hrs over a 36 hour time period, for a total of 13 time points. Striatal, cortical, hypothalamic and liver samples were harvested, flash frozen, and transferred to Expression Analysis for RNA extraction and miRNA-seq sequencing. Samples passing QC were analyzed to produce high quality, 50-base paired-end RNA-seq results.

overall_design: Striatal, cortical, hypothalamic and liver samples were collected from 26-week-old wild type C57BL/6J male mice every 3 hours for 36 hours, number of replicates 2 to 12 for each ZT group. miRNA-Seq was performed.

first: Jenny

last: Morton

first: Jim

last: Rosinski


title: High-throughput single-cell mitochondrial DNA genotyping reveals properties of clonal variation in human contexts [CRC_scATACseq]

status: Public on Jul 13 2020

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: Natural mitochondrial DNA (mtDNA) sequence variation plays a fundamental role in human disease and enables the clonal tracing of native human cells. While various genotyping approaches revealed mutational heterogeneity in human tissues and single cells, current methodologies are limited by scale. Here, we introduce a high-throughput, droplet-based mitochondrial single-cell Assay for Transposase Accessible Chromatin with sequencing (mtscATAC-seq) protocol and computational framework that facilitate high-confidence mtDNA mutation calling in thousands of single cells. Further, the concomitant high-quality accessible chromatin readout enables the paired inference of individual cell mtDNA heteroplasmy, clonal lineage, cell state, and accessible chromatin regulatory features. Our multi-omic analyses reveals single-cell variation in heteroplasmy of a pathologic mtDNA variant (m.8344A>G), which we tie to intra-individual chromatin variability and clonal evolution. Further, using somatic mtDNA mutations, we clonally trace thousands of hematopoietic cells in vitro and in patients with chronic lymphocytic leukemia, linking epigenomic variability to subclonal evolution in vivo.

overall_design: Colorectal cancer cells from a resection specimen were dissociated, stained for flow cytometry, gated on Zombie- CD235a- CD66b- cells which were sorted and further processed for mtscATAC-seq.

first: Leif

last: Ludwig


title: RNAseq analysis of distinct small intestinal cell populations isolated from Lgr5-EGFP C57BL/6 mice treated with NRG1

city: Clayton

first: David

middle: Richard

last: Powell

state: VIC

address: Wellington Road

department: Bioinformatics Platform

country: Australia

institute: Monash University

summary:
Purpose: The goal of the study was to investigate the effect of Neuregulin 1 (NRG1) on intestinal crypt-based columnar stem cells, their progenitors and differentiated cells.
Methods: Lgr5-EGFP C57BL/6 male mice (11-15 week-old, littermates) were injected with two intra-peritoneal doses of NRG1 daily (7.5 µg every 12 hours) or vehicle control (PBS) for 5 days (n=3). On day 6, small intestinal tissues were collected and several intestinal cell populations isolated by FACS based on Lgr5-GFP and CD24 expression [CBC stem cells (Lgr5high-CD24low), their immediate progenitors (Lgr5med-CD24low), subsequent progenitors (Lgr5low-CD24low) and differentiated cells (double negative)]. RNA was then extracted for each cell population and RNA sequencing analysis conducted.

overall_design: mRNA profiles of intestinal CBC stem cells, progenitor cells and differentiated cells isolated from NRG1-treated or PBS-treated mice were generated by RNA sequencing, in triplicate. Libraries of each biological replicate were prepared with 15ng of RNA using the Nugen Ovation RNA-Seq system V2 kit followed by Nugen Ovation Ultralow System V2 kit. High throughput sequencing was performed with HiSeq3000 with ~30 M reads targeted reads (single end 76nt length) per sample.

first: Thierry

last: Jardé

first: Helen

last: Abud


title: Activating PIK3CA  mutation promotes osteogenesis of bone marrow mesenchymal stem cells in macrodactyly

city: Shanghai

first: Hengqing

last: Cui

state: Shanghai

address: 639 Zhizaoju Road

institute: Shanghai 9th People's Hospital

summary: Comparison of differential expression between macrodactyly BMSC and polydactyly BMSC

overall_design: Total RNAs was extracted from passage 3 of cultured Macrodactyly-BMSCs (n=2) and Polydactyly-BMSCs (n=2) ,complementary DNA library preparation and sequencing were performed according to Illumina standard protocol.

first: Bin

last: wang


title: A single human VH gene endows for a broad-spectrum antibody response targeting bacterial lipopolysaccharides in the blood

first: Maya

last: Sangesland

state: MA

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT, and Harvard

summary: B cell receptors (BCRs) display a combination of variable (V) gene-encoded complementarity determining regions (CDRs) and adaptive/hypervariable CDR3 loops to engage antigens. It has long been proposed that the former naturally tune for recognition of pathogens or groups of pathogens. To mechanistically evaluate this within the human antibody repertoire, we performed immune challenges in transgenic mice bearing diverse human CDR3 and light chains, but were constrained to different human VH genes. We found that out of six commonly deployed VH sequences, only those CDRs encoded by IGHV1-2*02 enabled polyclonal antibody responses against bacterial lipopolysaccharide (LPS) when introduced to the bloodstream. LPS was prepared from diverse strains of gram-negative bacteria, and the VH gene-dependent responses were directed against the non-variable and universal saccrolipid substructure of this antigen. This reveals a broad-spectrum anti-LPS response in which germline-encoded CDRs naturally hardwire the human antibody repertoire for recognition of a conserved microbial target.

overall_design: Examination of antibody CDRH3 diversity within transgenic mice restricted to human IGHV1-69 or human IGHV1-2 VH genes and containing the human IgK locus.

first: Larance

last: Ronsard

first: Samuel

middle: W

last: Kazer

first: James

last: Gatter

first: Daniel

last: Lingwood


title: Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein

city: Würzburg

first: Jörg

last: Vogel

address: Josef-Schneider-Straße 2

department: Institute for Molecular Infection Biology

institute: Würzburg University

summary: coIP-seq of FopA in Salmonella enterica Typhimurium SL1344

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

overall_design: precipitation of wt and fopA::3xFLAG by monoclonal anti-FLAG M2 at OD 2.0 in LB media grown at 37 °C

first: Milan

last: Gerovac


title: The Disabled homolog 2 controls pro-metastatic activity of tumor-associated macrophages

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary: Tumor-associated macrophages (TAMs) are regulators of extracellular matrix (ECM) remodeling and metastatic progression, the main cause of cancer-associated death. We found that disabled 2 mitogen-responsive phosphoprotein (DAB2) is highly expressed in tumor-infiltrating TAMs and its genetic ablation significantly impairs lung metastasis formation. DAB2-expressing TAMs, mainly localized along the tumor invasive front, participate in integrin recycling, ECM remodeling and directional migration in a tridimensional matrix. DAB2+ macrophages escort the invasive dissemination of cancer cells by a mechanosensing pathway requiring the transcription factor Yes-Associated Protein. In human lobular breast and gastric carcinomas, DAB2+ TAMs correlated with a poor clinical outcome, identifying DAB2 as potential prognostic biomarker for cancer patient stratification. DAB2 is therefore central for the pro-metastatic activity of TAMs.

overall_design: Single cell transcrptome profiling of tumor-infiltrating myeloid cells from PyMT-WT and PyMT-Dab2 KO mice. Tumors pooled from 3 PyMT-WT and 3 PyMT-Dab2 KO mice were digested and myeloid cells were FACS sorted as CD45+lineage (CD3, CD19, NK1.1) negative cells. Sorted cell suspension was loaded on a GemCode Single Cell Instrument (10x Chromium System) to generate single cell GEMs. Single cell RNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library Kit v2 (10x Genomics).

first: Ilaria

last: Marigo

first: Rosalinda

last: Trovato

first: Vincenzo

last: Bronte


title: S1-Domain RNA Binding Protein (CvfD) Is a New Post-Transcriptional Regulator That Mediates Cold Shock, Phosphate Transport, and Virulence in Streptococcus pneumoniae D39

city: Bloomington

first: Malcolm

last: Winkler

state: IN

address: 1001 E. Third Street

department: Biology

institute: Indiana University

summary: Post-transcriptional gene regulation often involves RNA-binding proteins that modulate mRNA translation and/or stability either directly through protein-RNA interactions or indirectly by facilitating the annealing of small regulatory RNAs (sRNAs). The human pathogen Streptococcus pneumoniae D39 (pneumococcus) does not encode in its genome any homologs to RNA-binding proteins known to be involved in promoting sRNA stability and function, such as Hfq or ProQ, even though it contains genes for at least 112 sRNAs. Instead, the pneumococcal genome contains genes for at least six S1 RNA-binding domain proteins, which includes ribosomal protein S1 (rpsA), polynucleotide phosphorylase (pnpA), RNase R (rnr), and three proteins of unknown function. Here, we characterize the function of one of these conserved, yet uncharacterized S1-domain proteins, SPD_1366, which we have renamed CvfD (Conserved virulence factor D), since loss of this protein results in a attenuation of virulence in a murine pneumonia model. We also report that deletion of cvfD impacts expression of 144 transcripts including the pst1 operon, encoding the phosphate transport system 1 in S. pneumoniae. We further show that CvfD post-transcriptionally regulates the PhoU2 master regulator of the pneumococcal dual phosphate transport system by binding phoU2 mRNA and impacting translation. CvfD not only controls expression of phosphate transporter genes, but also functions as a global regulator impacting cold sensitivity and the expression of sRNAs and genes involved in diverse cellular functions, including manganese uptake and zinc efflux. Together, our data suggest that CvfD exerts a broad impact on pneumococcal physiology and virulence via post-transcriptional gene regulation.

overall_design: Characterization of S1-domain RNA Binding Protein (CvfD) in Streptococcus pneumoniae D39 using RNA-seq. Wildtype S. pneumoniae strain and its derived cvfD mutants were tested in triplicates.

first: Douglas

last: Rusch

middle: E


title: Involvement of Arabidopsis BIG protein in cell death mediated by Myo-Inositol homeostasis

city: Gif-sur-Yvette

first: Déborah

last: MANZA MIANZA

address: 630 Rue Noetzlin

country: France

institute: Institut des Sciences des Plantes - Paris Saclay

summary:
Programmed cell death (PCD) is essential for several aspects of plant life. We previously identified the mips1 mutant of Arabidopsis thaliana, which is deficient for the enzyme catalyzing myo-inositol synthesis, that displays light-dependent formation of lesions on leaves due to Salicylic Acid (SA) over-accumulation. Rationale of this work was to identify novel regulators of plant PCD using a genetic approach.
A screen for secondary mutations that abolish the mips1 PCD phenotype identified a mutation in the BIG gene, encoding a factor of unknown molecular function that was previously shown to play pleiotropic roles in plant development and defence. Physiological analyses showed that BIG is required for lesion formation in mips1 via SA-dependant signalling. big mutations partly rescued transcriptomic and metabolomics perturbations as stress-related phytohormones homeostasis.
In addition, since loss of function of the ceramide synthase LOH2 was not able to abolish cell death induction in mips1, we show that PCD induction is not fully dependent of sphingolipid accumulation as previously suggested.
Our results provide further insights into the role of the BIG protein in the control of MIPS1-dependent cell death and also into the impact of sphingolipid homeostasis in this pathway.

overall_design: Arabidopsis thaliana ecotype Colombia (Col-0) and big and mips1 and double mutant big mips1 were used in this study.

first: Quentin

last: Bruggeman

first: Florence

last: Piron-Prunier

first: Frédérique

last: Tellier

first: Jean-Denis

last: Faure

first: David

last: Latrasse

last: Manza-Mianza

first: Christelle

last: Mazubert

first: Sylvie

last: Citerne

first: Stéphanie

last: Boutet-Mercey

first: Raphael

last: Lugan

first: Catherine

last: Bergounioux

first: Cécile

last: Raynaud

first: Moussa

last: Benhamed

first: Marianne

last: Delarue


title: Single cell and population transcriptomics reveal epithelial remodeling in type 2-high asthma

city: Denver

first: Nathan

last: Jackson

state: CO

address: 1400 Jackson St.

department: Center for Genes, Environment, and Health

institute: National Jewish Health

summary: BACKGROUND: The type 2 cytokine-high asthma endotype (T2H) is characterized by IL-13-driven mucus obstruction of the airways. To investigate this poorly understood pathobiology, we characterized IL-13 effects on human airway epithelial cultures using single cell RNA-sequencing, finding that IL-13 generated a novel transcriptional state for each cell type. Specifically, we discovered a mucus secretory program induced by IL-13 in all cell types which converted both mucus and defense secretory cells into a metaplastic state with emergent mucin production and secretion, while leading to ER stress and cell death in ciliated cells. The IL-13-remodeled epithelium secreted a pathologic, mucin-imbalanced, and innate immunity-depleted proteome that arrested mucociliary motion. Signatures of IL-13-induced cellular remodeling were mirrored by transcriptional signatures characteristic of the nasal airway epithelium within T2H versus T2-low asthmatic children. Our results reveal the epithelium-wide scope of T2H asthma and present novel therapeutic targets for restoring normal epithelial function.

overall_design: Single cell transcriptomics was carried out for experiments involving either acute (48 hours) or chronic (11 days) stimulation with IL-13 (or mock stimulation with BSA) of air-liquid interface (ALI) cultures grown from epithelial cells taken from two tracheal donors. For the acute stimulation experiment, we sequenced a total of 2,385 cells,  plus positive and negative controls (1,894 remaining after QC). For the chronic stimulation experiment, we sequenced a total of 802 single cells (756 remaining after QC and batch correction).

middle: D

first: Jamie

middle: L

last: Everman

first: Maurizio

last: Chioccioli

first: Katherine

last: Goldfarbmuren

first: Satria

last: Sajuthi

first: Cydney

last: Rios

first: Roger

last: Powell

first: Michael

last: Armstrong

first: Joe

last: Gomez

first: Cole

last: Michel

first: Celeste

last: Eng

first: Sam

last: Oh

first: Jose

last: Rodriguez-Santana

first: Luigi

last: Feriani

first: Pietro

last: Cicuta

first: Nichole

last: Reisdorph

first: Esteban

last: Burchard

first: Max

middle: A

last: Seibold


title: Tuft cells restrain pancreatic tumorigenesis through paracrine eicosanoid signaling

city: La Jolla

first: Zhibo

last: Ma

state: California

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

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

overall_design: Refer to individual Series


title: Tuft cells restrain pancreatic tumorigenesis through paracrine eicosanoid signaling [bulk RNA-seq]

summary: We performed bulk RNA-seq on pancreatic and intestinal tuft cells, bone marrow derived macrophages with various treatments, and mouse pancreatic stellate cells with various treatments.

overall_design: The transcriptomes of pancreatic and intestinal tuft cells, bone marrow derived macrophages, and pancreatic stellate cells were profiled. Three biological replicates for each cell type.

first: Geoffrey

last: Wahl

first: Kathleen

last: DelGiorno

first: Chi-Yeh

last: Chung


title: Tuft cells restrain pancreatic tumorigenesis through paracrine eicosanoid signaling [single-cell RNA-seq]

summary: We performed Smart-seq2 scRNAseq on 156 pancreatic tuft cells . We also profiled FACS sorted EpCAM+;CD45+ immune cells and EpCAM-;CD45- non-immune stroma cells from  from 3 caerulein-treated KC and 2 caerulein-treated KPouC pancreata by using the 10X Genomics 3' scRNAseq v3.1 kit.

overall_design: single cell transcriptional profiling of pancreatic tuft cells using Smart-seq2 platform, and immume + stromal cells from caerulein-treated KC and KPouC mice pancreas.

first: Nikki

last: Lytle


title: Role of TET1 Mediatd 5hmC in Osteoarthritis [RRHP]

city: Stanford

first: Fiorella

last: Grandi

address: 300 Pasteur Drive

department: Orthopedic Surgery

institute: Stanford University

type: Methylation profiling by high throughput sequencing

summary: No disease-modifying drugs exist to treat osteoarthritis (OA), a degenerative disease of the joint.  The complexity of OA necessitates a combinational and broad therapeutic approach. Epigenetic regulators are able to control large programs of genes, and recent work from our group and others have showcased systemic epigenetic dysregulation in OA. Previously, we demonstrated that OA chondrocytes accumulate 5-fold more 5-hydroxymethylcytosine (5hmC), an oxidized derivative of methylcytosine (5mC) associated with gene activation, at disease relevant sites. To test if 5hmC has a role in the early onset of OA, we utilized a mouse model of surgically induced OA, destabilization of the medial meniscus (DMM), and found that DMM mice gained ~40,000 differentially hydroxymethylated sites. Genetic loss of TET1, the enzyme responsible for 5hmC deposition, prevented pathologic gain of 5hmC, activation of many OA pathways, and protected mice from OA development. To test the clinical potential of a TET1 based OA therapy, we injected 2-hydroxyglutarate (2-HG), a TET inhibitor, into the joint after DMM induction and  observed stalled disease progression. Collectively, these data show that TET1 mediated 5hmC deposition regulates multiple OA pathways and that its modulation can be a powerful clinical tool for OA.

overall_design: DMM was induced on male mice 3-4 months of age. DNA was extracted from the joint at 6 post surgery. Age-matched sham controls are also included. All groups contain 3 biological replicates. 5hmC was measured at CCGG sites using reduced representation hydroxymethylation sequencing (RRHP) from Zymo. A negative control (Neg_control) without treatment with the B-Galc enzyme is included to give the background signal for this technique.

first: Piera

last: Smeriglio

first: Nidhi

last: Bhutani


title: Inhibition of TET1 prevents the development of Osteoarthritis and reveals the 5hmC landscape that orchestrates pathogenesis


title: Role of TET1 Mediated 5hmC in Osteoarthritis [RNA-seq]

overall_design: DMM was induced on male mice 3-4 months of age. RNA was extracted from the joint at 6 or 12 weeks post surgery. Age-matched sham controls are also included. All groups contain 3 biological replicates, except 6weeks sham (n=2).


title: Comprehensive transcriptome analysis of human myofibroblasts with/without the JQ-1 treatment

city: Chiba

first: Yoshitoshi

last: Kasuya

address: 1-8-1 Inohana Chuo-ku

department: Grad. Sch. Med

country: Japan

institute: Chiba Univ.


title: High-throughput single-cell mitochondrial DNA genotyping reveals properties of clonal variation in human contexts [CD34-PBMC-invivo-scATAC]

first: Caleb

last: Lareau

overall_design: CD34+ cells were derived from a 47 year old healthy volunteer. After ~3 months, additional peripheral blood mononuclear cells (PBMCs) were obtained. Two replicates of each population were profiled with mtscATAC-seq.

first: Leif

last: Ludwig


title: LncRNA and mRNA expression profile in hepatocellular carcinoma patient paired tissues

city: Singapore

first: Caroline G.

last: Lee

address: MD7, Level 2, 8 Medical Drive

country: Singapore

institute: National University of Singapore

summary: This study aimed to identify differential expression of lncRNAs and mRNAs in hepatocellular carcinoma patient tissues and potential regulation of mRNAs by lncRNAs.

overall_design: Arraystar LncRNA human V4 microarray was performed on total RNA that was extracted from 49 hepatocellular carinoma patient tumor tissues and adjacent non-tumor tissues.

first: Lee

middle: J

last: Lim

first: Alexander

middle: Y

first: Brian

middle: K

last: Goh

first: Pierce

last: Chow

first: C

last: Chan

first: P

middle: C

last: Cheow

first: S

first: Tony

first: London

last: LPJOoi

first: Caroline

middle: G


title: Pervasive changes of mRNA splicing in upf1 deficient zebrafish identify rpl10a as a regulator of T cell development

city: Freiburg im Breisgau

first: Thomas

last: Boehm

address: Stübeweg 51

institute: MPI-IE Freiburg

summary: The transcriptome of eukaryotic cells is constantly monitored for errors to avoid the production of undesired protein variants. The evolutionarily conserved nonsense-mediated mRNA decay (NMD) pathway degrades aberrant mRNAs, but also functions in the regulation of transcript abundance in response to changed physiological states. As a result of its essential functions, only few animal models of impaired NMD activity have been developed. Here, we describe a zebrafish mutant of upf1, encoding the central component of the NMD machinery. Fish homozygous for the upf1t20450 allele (Y163X) survive until day 10 after fertilization, presenting with impaired T cell development as one of the most conspicuous features of the mutant phenotype. Analysis of differentially expressed genes identified dysregulation of the pre-mRNA splicing pathway, accompanied by perturbed auto-regulation of canonical splicing activators (SRSF) and repressors (HNRNP). In upf1-deficient mutants, NMD-susceptible transcripts of ribosomal proteins that are known for their role as non-canonical splicing regulators were greatly increased, most notably, rpl10a. When the levels of NMD-susceptible rpl10a transcripts were artifically increased in zebrafish morphants, T cell development was significantly impaired, suggesting that perturbed autoregulation of rpl10a splicing contributes to failing T cell development in upf1 deficiency. Our results identify an extra-ribosomal tissue-specific function to rpl10a in the immune system, and thus exemplify the advantages of the zebrafish model to study the effects of upf1-deficiency in the context of a vertebrate organism.

overall_design: The experiments aimed at identifying the role of the upf1 gene in lymphocyte development of zebrafish. The transcriptomes of wild-type and upf1 mutant fish at 5 days after fertilization were compared for differences in expression levels

first: D

last: Lawir

first: K

last: Sikora

first: T


title: High-throughput single-cell mitochondrial DNA genotyping reveals properties of clonal variation in human contexts [CD34-invitro]

first: Caleb

overall_design: ~500 or 800 CD34+ hematopoietic stem and progenitor cells were clonally expanded in two independent cultures before differentiating cells in the presence of erythropoietin, stem cell factor and interleukin-3.


title: High-throughput single-cell mitochondrial DNA genotyping reveals properties of clonal variation in human contexts [CLL-scRNA]

overall_design: Peripheral blood mononuclear cells were obtained from human patients diagnosed with chronic lymphocytic leukemia and processed for 10x scRNA-seq.

first: Leif


title: High-throughput single-cell mitochondrial DNA genotyping reveals properties of clonal variation in human contexts [CLL-scATAC]

overall_design: Peripheral blood mononuclear cells were obtained from two human patients diagnosed with chronic lymphocytic leukemia and processed for 10x scATAC-seq


title: Mechanistic insights into chromatin targeting by leukemic NUP98-PHF23 fusion

city: Chapel Hill

first: Yiran

last: Guo

state: North Carolina

address: 450 West Drive

department: GMB

institute: UNC

summary: The dysregulation of plant homeodomain (PHD) fingers has been implicated in several human diseases, including cancer. In a subset of aggressive acute myeloid leukemia (AML), chromosomal translocations that involve nucleoporin 98 (NUP98), a component of the nuclear pore complex, and a PHD finger-containing protein, such as KDM5A/JARID1A, PHF23 and BPTF, generate potent oncoproteins (namely NUP98-KDM5A, NUP98-PHF23 and NUP98-BPTF; or together termed as NUP98-PHD fusions) that are able to arrest hematopoietic differentiation and induce acute myeloid leukemia in murine models. In these processes, a PHD finger that specifically recognizes H3K4me3/2 marks was essential for leukemogenesis. Mutations in PHD fingers that abrogated H3K4me3 binding also abolished leukemic transformation. An overlap of NUP98-KDM5A oncoprotein binding sites and H3K4me3-positive loci at the Hoxa/b gene clusters and Meis1 in ChIP-seq together with NMR analysis of the H3K4me3-binding sites of the PHD fingers from PHF23, KDM5A and BPTF suggests a common PHD finger-dependent mechanism that promotes leukemogenesis by this type of NUP98-PHD finger fusions. Disulfiram (DS), a small molecule compound that directly targets the PHD finger, shows anti-proliferation effects in AML cells expressing NUP98-PHD through the conserved inhibitory mechanism. Our findings highlight the direct correlation between the abilities of NUP98-PHD finger fusion chimeras to associate with H3K4me3-enriched chromatin and leukemic transformation.

overall_design: ChIP-seq was carried out to map out genome-wide binding of FLAG-tagged NUP98-KDM5A (N5A) and two histone marks (H3K4me3 and H3K27me3) in the murine AML cells transformed by N5A. Two replicates of FLAG ChIP-seq experiments were done for N5A.

first: Greg

last: Wang


title: DNA methylation during seed development in small-seeded chickpea

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

institute: Jawaharlal Nehru University

summary: In this study, we performed bisulphite of two stages of seed development in a small-seeded chickpea cultivar (Himchana 1) using Illumina platform. Paired-end reads were generated from 5 libraries. Data obtained in FASTQ files were pre-processed to remove adapters and low-quality reads.  We identified methylation level at each cytosine residue covered in sequencing and differentially methylated regions (DMRs) between stages of seed development.

overall_design: Genomic DNA was extracted from all the samples were fragmented to a mean size of 200-500 bp via sonication followed by sodium bisulphite conversion (DNA Methylation-GoldTM Kit, Zymo Research). TrueSeq-methylated adaptors were ligated and sequenced using Illumina HiSeq platform. Adapters and low-quality reads were removed using NGS QC Toolkit (v2.3). High-quality filtered reads were mapped on kabuli reference genome using Bismark (v0.14.3). Methylation level in each cytosine residue(s) and differentially methylated regions (DMRs) were detected using Methylkit (v0.5.6).

first: Rohini

last: Garg

first: Khushboo

last: Gupta

first: Niraj

last: Khemka

first: Mohan

last: Rajkumar


title: Glycine max Alternatively Spliced Transcript Detecting Microarray (GmASDM).

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

country: South Korea

institute: GreenGene Biotech Inc.

summary: Plants remember what they have experienced and are thereby able to confront repeated stresses more promptly and strongly. A subset of genes showed increased transcript levels under drought stress conditions, followed by a return to basal levels during recovery (watered) states, and then displayed elevated levels again under subsequent drought conditions. To screen for a set of drought stress memory genes in soybean (Glycine max L. cv. Daepoong), we designed a 180K DNA chip comprising 60-bp probes synthesized in situ to examine 55,588 loci. Through microarray analysis using the DNA chip, we identified 2,165 and 2,385 genes with more than 4-fold increases or decreases in transcript levels, respectively, under initial (first) drought stress conditions, when compared with the non-treated control. The transcript levels of the genes returned to basal levels during recovery (watered) states, then 677 and 987 genes displayed more than 16-fold elevated or reduced levels, respectively, under subsequent (second) drought conditions, when compared to the non-treated control. Gene Ontology analysis classified the drought stress memory genes into several functional categories, including those involved in trehalose biosynthesis and drought tolerance responses. We selected a number of drought stress memory genes encoding various transcription factors, protein phosphatase 2Cs, and late embryogenesis abundant proteins, and confirmed the microarray data by quantitative reverse-transcription real-time PCR. Upon repeated watering and subsequent (third) drought treatment, the elevated levels of the drought stress memory gene transcripts were propagated into newly developed second leaves, although at reduced levels when compared to the second drought treatment on the first leaves.

overall_design: Based on the whole soybean (G. max var. Williams 82) genome database available from Phytozome (http://www.phytozome.net) (Goodstein et al. 2011), three 60-nt-long feature probes were designed from a representative transcript of each gene, beginning 60 bp upstream from the end of the stop codon and shifting downstream at 30-bp intervals; the three resulting probes covered 120 bp: 60 bp of coding sequence (CDS) and 60 bp in the 3' untranslated region (3'-UTR). Additional probes for alternatively spliced transcripts, chloroplast genes, mitochondrial genes, and selection markers such as gfp, gus, hyg, bar, and kan were included. A total of 175,391 probes were designed and synthesized in situ on the 180K DNA chip, which was manufactured by Agilent Co. (Santa Clara, CA, USA).

first: Jong-Joo

last: Cheong


title: High- and low-protein diet: effects on human hepatic fat content, autophagy, mitochondrial function and fat metabolism

city: Odense M

first: Anne

last: Loft

address: Campusvej 55

department: Biochemistry & Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Non-alcoholic fatty liver disease (NAFLD) is becoming increasingly prevalent and nutrition intervention remains the most important therapeutic approach for NAFLD. Our aim was to investigate whether low- (LP) or high-protein (HP) diets are more effective in reducing liver fat and reversing NAFLD. Here RNA-seq analysis was used to analyse which metabolic pathways that were altered on the LP and HP diets.

overall_design: 19 morbidly obese subjects undergoing bariatric surgery were randomized into two hypocaloric (1500 kcal/day) diet groups, a low protein (LP: 10 E% protein, n=10) and a high protein (HP: 30 E% protein, n=9), for three weeks prior to surgery. RNA-seq analyses were performed on liver samples collected during surgery.

first: Chenchen

last: Xu

first: Mariya

last: Markova

first: Stephan

last: Herzig

first: Olga

last: Pivovarova-Ramich

first: Andreas

last: Pfeiffer


title: DNA methylation during seed development in large-seeded chickpea

summary: In this study, we performed bisulphite of five stages of seed development in a large-seeded chickpea cultivar (JGK 3) using Illumina platform. Paired-end reads were generated from 11 libraries. Data obtained in FASTQ files were pre-processed to remove adapters and low-quality reads.  We identified methylation level at each cytosine residue covered in sequencing and differentially methylated regions (DMRs) between stages of seed development.


title: Competition between 3’ end maturation and degradation drives snRNA quality control

first: Rea

last: Lardelli

state: CA

address: 9500 Gilman Dr

institute: UCSD

summary: Polymerases and exonucleases act on 3’ ends of nascent RNAs to promote their maturation or degradation but how the balance between these activities is controlled to dictate the fates of cellular RNAs remains poorly understood. Here, we identify a central role for the human DEDD deadenylase TOE1 in distingushing the fates of small nuclear (sn)RNAs of the spliceosome from genome-encoded snRNA variants. We find that TOE1 promotes maturation of all regular RNA polymerase II-transcribed snRNAs of the major and minor spliceosomes by removing post-transcriptional oligo(A)-tails, trimming 3’ ends, and preventing nuclear exosome targeting. By contrast, TOE1 promotes little to no maturation of tested U1 variant snRNAs, which are instead targeted by the nuclear exosome. These observations suggest that TOE1 is positioned at the center of a 3’ end quality control pathway that selectively promotes maturation and stability of regular snRNAs while leaving snRNA variants unprocessed and exposed to degradation in what could be a widespread mechanism of RNA quality control given the large number of non-coding RNAs processed by DEDD deadenylases.

overall_design: We performed experiments to profile 3' ends of U1, U2, U4, U5, U4atac, U11, U12, U3, and U8 RNAs. Samples profiled include immunopurified RNA, purified nascent RNA, and total RNA from HEK293 cells which were subject to various treaments including depletion of TOE1-degron and siRNA depletion of components of the nuclear exosome.

first: Jens

last: Lykke-Andersen


title: A non-Dicer RNase III and four other novel factors required for RNAi-mediated transposon suppression in the human pathogenic yeast C. neoformans

city: San Francisco

first: Jordan

middle: Emily

last: Burke

address: N374 Genentech Hall, 600 16th Street

department: Biochemistry and Biophysics

institute: University of California, San Francisco

summary: The human pathogenic yeast Cryptococcus neoformans silences transposable elements using endo-siRNAs and an Argonaute, Ago1. Endo-siRNAs production requires the RNA-dependent RNA polymerase, Rdp1, and two partially redundant Dicer enzymes, Dcr1 and Dcr2, but is independent of histone H3 lysine 9 methylation. We describe here an insertional mutagenesis screen for factors required to suppress the mobilization of the C. neoformans HARBINGER family DNA transposon HAR1. Validation experiments uncovered five novel genes (RDE1-5) required for HAR1 suppression and global production of suppressive endo-siRNAs. The RDE genes impact global siRNA levels and transposon mobilization but not global transcript levels, suggesting the endo-siRNAs do not act by impacting target transcript synthesis or turnover.  RDE3 encodes a non-Dicer RNase III related to S. cerevisiae Rnt1, RDE4 encodes a predicted terminal nucleotidyltransferase, while RDE5 has no strongly predicted encoded domains.  Affinity purification-mass spectrometry studies reveal that Rde3 and Rde5 are physically associated. RDE1 encodes a G-patch protein homologous to the S. cerevisiae Sqs1/Pfa1, a nucleolar protein that directly activates the essential helicase Prp43 during rRNA biogenesis.  Rde1 copurifies Rde2, another novel protein obtained in the screen, as well as Ago1, a homolog of Prp43, and numerous predicted nucleolar proteins. We also describe the isolation of conditional alleles of PRP43, which are defective in RNAi. This work reveals unanticipated requirements for a non-Dicer RNase III and presumptive nucleolar factors for endo-siRNA biogenesis and transposon mobilization suppression in C. neoformans.

overall_design: Insertional mutagenic screen, QuantSeq and small RNA-seq to identify and characterize novel RNAi factors

first: Hiten

last: Madhani


title: Intracellular and extracellular galectin-9 induces STING degradation and promotes suppressive myeloid cell expansion in human tumor-bearing host

city: Guangzhou

first: Jiang

last: Li

state: Guangdong

address: Dongfengdong Road NO.651, Yuexiu District

institute: State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center

summary: Galectin-9 (Gal-9) is a versatile immuno-modulatory protein. Its contribution to the expansion of suppressive myeloid cells in human tumors remain to be investigated. For this aim, we used in vitro models bringing together carcinoma cells derived from nasopharyngeal carcinomas (NPC) and CD33+ myeloid precursors. We found that Gal-9 expression in carcinoma cells enhances the generation of HLA-DR-CD33+CD11b+ myeloid-derived suppressor cells (MDSCs) in bystander cells. The underlying mechanisms involve both the intra-cellular and secreted Gal-9. Inside carcinoma cells, Gal-9 up-regulates the expression of a variety of pro-inflammatory cytokines which are critical for MDSC differentiation and recruitment, including IL-1b, IL-6, CCL22, and CX3CL1. This effect is mediated by accelerated degradation of the STING protein resulting from direct interaction of the Gal-9 carbohydrate recognition domain 1 with the STING C-terminus and subsequent enhancement of the TRIMP29-mediated K48-linked ubiquitination of STING. Moreover, we showed that extracellular Gal-9 secreted by carcinoma cells can enter the myeloid cells and trigger the same signaling cascade.  Consistently, clinical data from NPC patients show that high concentrations of Gal-9 in tumor cells and plasma samples are associated with shortened disease-free survival. These findings unearth a novel contribution of Gal-9 to the generation of an immunosuppressive microenvironment which favors tumor development.

overall_design: Examination of 2 different human nasopharyngeal carcinomas cells.

first: Li

last: Jiang

first: Zhang

last: Chuanxia


title: Cadmium interference with iron sensing reveals transcriptional programs sensitive and insensitive to reactive oxygen species

city: Columbia

first: Samuel

middle: Alonzo

last: McInturf

state: Missouri

address: 1201 Rollins Street

department: Plant Sciences

institute: University of Missouri - Columbia

summary: Iron (Fe) is an essential micronutrient whose uptake is tightly regulated to balance both deficiency and Fe excess induced oxidative stress. The non-essential heavy metal cadmium (Cd) both induces oxidative stress and an Fe deficiency like response.  It is unclear how Cd induces this response, nor how it relates to Fe status sensing.  Using next generation sequencing, H2O2 quantification in both wild type and the Fe over-accumulating mutant opt3-2, we explored how Cd interferes with Fe sensing.  We found a large overlap of genes consistently responsive to Fe deficiency and Cd in both leaves and roots.  Two subnetworks emerged dependent on the high Fe and H2O2 concentration in opt3-2, while opt3-2 chloroplasts showed reduced photosynthetic efficiency during Cd exposure, indicating that they are one source of H2O2.  We describe the hierarchical regulation of Fe deficiency responses in the context of the opt3-2 mutant, and demonstrate that the opt3 dependent induction of Fe deficiency responses can be negated, or even reversed, by H2O2 dependent signaling, while the high Fe content of opt3-2 indicates Cd induced iron deficiency is not a function of reduced Fe uptake, but rather the putative leaf Fe sensor is Cd liable.

overall_design: Wild type (Col-0) and opt3-2 were subjected or not to 20uM CdCl2 in hydroponic culture for 72hr.  mRNA from leaves and root were isolated seperately and sequenced on a Illumina Hiseq.  Three biological replicates were sequenced for each sample type.

first: David

last: Mendoza-Cózatl


title: Transcriptome Patterns in Hidradenitis Suppurativa: Support for the Role of Antimicrobial Peptides and Interferon Pathways in Disease Pathogenesis

city: Washington

first: Victoria

middle: Kate

last: Shanmugam

state: DC

address: 2300 M Street, NW

department: Division of Rheumatology

institute: The George Washington University School of Medicine and Health Sciences

summary:
Comparison of transcriptome of HS samples and Abdominoplasty skin
Aim: The purpose of this study was to harness mRNA expression arrays to investigate the transcriptome profile in HS compared to control skin.

overall_design: Methods: Illumina HumanHT-12 v4 Expression Bead Chips were used to measure mRNA expression in skin samples from HS (n=10) and abdominoplasty skin specimens (n=11).

first: Derek

last: Jones

first: Sean

last: McNish

first: Matthew

last: Bendall

first: Keith

last: Crandall


title: Untangling determinants of health and lifespan

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: The impact of chronic caloric restriction (CR) on health and survival in model organisms is complex and its underlying molecular mechanisms are poorly understood. Genetic background, sex, degree of CR and diet composition are expected modifiers of survival outcomes of this intervention. A recent study in mice addressed the impact of diet composition and feeding patterns used in nonhuman primates. It was found that, while diet composition alone did not impact longevity, fasting and calories were determinant for increased survival. We use here a combined physiological, multi-omics (transcriptomics-metabolomics), and integrated pathway analyses to gain insight into core and specific pathways associated with liver healthspan and lifespan. Main findings show that liver longevity pathways associated with CR predominantly correspond to detoxification, molecular turnover-repair-maintenance, and energy supply processes. Differential responses on lifespan extension provided by the different feeding strategies unveiled a distinct pattern of longevity pathways that centered around amino acid, fatty acid and nucleic acid metabolisms. Glycine-serine-threonine metabolism was a unique metabolic hub associated with lifespan whereas short-chain fatty acids and essential PUFAs metabolism were unique to healthspan. Nonhuman primate serum metabolomics data essentially recapitulated key features in mice.

overall_design: This microarray study of liver gene expression from three feeding regimens, ad libitum (AL), 30% caloric restriction (CR), or meal-fed (MF), in male C57BL6/J mice examines the transcriptional effects on mice who were fed either an open source diet (NIA diet) low in sucrose and fat, or a sucrose-rich diet (WIS diet) composed of purified ingredients from five monts of age and for the remainder of their lives. There were from four to nine biological replicates for each of the six different combinations of diet and feeding regimens, for a total of forty-eight microarray samples.

first: Miguel

last: Aon

first: Michel

last: Bernier

first: Sarah

last: Mitchell

first: Clara

last: Di Germanio

first: Julie

last: Mattison

first: Margaux

last: Ehrlich

first: Ricky

last: Colman

first: Rozalyn

last: Anderson

first: Rafael

last: de Cabo


title: Comparative transcriptomic and proteomic analyses provide insights into functional genes for hypoxic adaptation in embryos of Tibetan chickens

city: Beijing

first: Ying

last: Zhang

address: Haidian District, Yuanmingyuan West Road 2

institute: China Agricultural University

summary: Background/Aims: Tibetan chickens, a unique plateau breed, have good performances to adapt to high-altitude hypoxic environments. A number of positively selected genes have been reported in Tibetan chickens; however, the mechanisms of gene expression for hypoxia adaptation are not fully understood. Methods: Eggs from Tibetan (TC) and Chahua (CH) chickens were incubated under hypoxic and normoxic conditions, and vessel density index (VDI) in the chorioallantoic membrane (CAM) of embryos was measured. Meanwhile, Transcriptomic and proteomic analyses of CAM tissues were performed in TC and CH embryos under hypoxic incubation using RNA-seq and iTRAQ. Results: We found that the vessel density index (VDI) in CAM of TCs was lower than in CHs under hypoxia incubation.  In the transcriptomic and proteomic analyses, 160 differentially expressed genes (DEGs) and 387 differentially expressed proteins (DEPs) that were mainly enriched in angiogenesis, vasculature development, blood vessel morphogenesis, blood circulation, renin-angiotensin system, and HIF-1 and VEGF signaling pathways. Twenty-six genes involved in angiogenesis and blood circulation, two genes involved in ion transport, and six genes that regulated energy metabolism were identified as candidate functional genes in regulating hypoxic adaption of chicken embryos. Conclusion: Combination of transcriptomic and proteomic data revealed several key candidate regulators and pathways that might play high-priority roles in the hypoxic adaptation of Tibetan chickens by regulating angiogenesis and promoting blood circulation, thus explaining the blunt responses to hypoxic conditions on CAM angiogenesis in Tibetan chicken embryos. This research provided insights into the molecular mechanism of hypoxia adaptation in Tibetan chickens.

overall_design: Chorioallantoic membrane (CAM) of embryos mRNA profiles of 11-day old Tibetan chickens (TCs) and Chahua chickens (CHs) were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000 platform.

first: Yawen

first: Hongliang

first: Xuyuan


title: RNAseq of Plasmodium falciparum 3D7 parasites treated with the Jumonji pan inhibitor JIB-04

status: Public on Jul 12 2020

city: Dallas

first: Elisabeth

last: Martinez

state: Texas

address: 6000 Harry  Hines Blvd.

department: Department of Pharmacology

institute: UT Southwestern Medical Center

summary: Little is known about the role of the three Jumonji C (JmjC) enzymes in Plasmodium falciparum (Pf). Here, we show that JIB-04 and other established inhibitors of mammalian JmjC histone demethylases kill asexual blood stage parasites and are even more potent at blocking gametocyte development and gamete formation. In late stage parasites, JIB-04 increased levels of trimethylated lysine residues on histones, suggesting the inhibition of P. falciparum Jumonji demethylase activity. These epigenetic defects coincide with deregulation of invasion, cell motor, and sexual development gene programs, including gene targets coregulated by the PfAP2-I transcription factor and chromatin-binding factor, PfBDP1. Mechanistically, we demonstrate that PfJmj3 converts 2-oxoglutarate to succinate in an iron-dependent manner consistent with mammalian Jumonji enzymes, and this catalytic activity is inhibited by JIB-04 and other Jumonji inhibitors. Our pharmacological studies of Jumonji activity in the malaria parasite provide evidence that inhibition of these enzymatic activities is detrimental to the parasite.

overall_design: Trophozoite stage (29 hpi +/- 2h) Plasmodium falciparum 3D7 parasites were treated with 4.5 uM JIB-04 E, JIB-04 Z, or vehicle for 6 hours.  Total RNA was isolated from starting culture (0h) and after treatment (+6h) and libraries were prepared from poly-A selected RNA using the TruSeq Stranded mRNA Library Prep kit from Illumina.   A total of 16 samples (4 treatments with 4 replicates) were sequenced.

first: Krista

last: Matthews


title: Different lipid forms of omega-3 and their effect on small intestine in mice

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

summary: Omega - 3 fatty acids of marine origin exert beneficial effects on lipid metabolism and can protect against insulin resistance in high fat diet (HFD)-fed animals. Simultaneously, recent studies showed that different lipid forms could have  numerous  consequences  regarding  the  regulation  of  energy balance,  nutrient  absorption, and  substrate  metabolism. Indeed, when omega-3 was provided as triglycerides (TG, i.e. fish  oil), it induced dose-dependently the  expression  of  genes involved  in  lipid  metabolism  as  well  as  fatty  acid  oxidation in  small intestine  of  C57BL/6  mice  fed  various  HFDs.   As the  underlying  mechanism(s)  explaining  the  differences  in  EPA/DHA  bioavailability among  various  lipid  forms  of  Omega-3  is  not  entirely  clear, we performed a mouse study (n=8 per group) using purified HFDs with control HFD based on corn oil (cHF) and part of the lipids were replaced by omega-3 fish lipids in different forms: as either TG (cHF-F), marine phospholipids (PL; Krill oil, given at two different doses Krill-low (Krill-L) and Krill-high (Krill-H)), and as wax esters in the extract from the zooplankton Calanus finmarchicus (Calanus oil CAL-L representing same omega-3 levels as Krill-L diet). As a healthy control we fed a subset of mice standard chow (STD). All mice were fed their diet for 8 weeks and after sacrifice, whole small intestine was isolated, frozen and used for RNA isolation and microarray gene expression analysis using 8x60K Agilent arrays. Results showed that PL-H versus control cHFc induced specifically metabolic lipid pathways, while TG and PL-L mainly affected cytoskeleton regulation.

overall_design: Adult male C57BL/6N mice were initially fed cHF diet (except STD group) for one week and then fed experimetal diets (cHF, cHF-F, Krill - H, Krill-L and CAL-L) for 8 weeks. After sacrifice, whole small intestine was rapidly removed,opened on cold pad ,gently wiped of the remains of lumenal content,  weighed, and frozen in liquid nitrogen and used for RNA isolation and whole genome gene expression microarray hybridisation using Agilent 8x60K arrays.

first: Petra

last: Kucharikova

first: Annelies

last: Bunschoten

first: Olga

last: Horakova

first: Martin

last: Rossmeisl

first: Jan

last: Kopecky

first: Jaap

last: Keijer


title: Genetic deletion of microRNA biogenesis in muscle cells reveals a hierarchical non- clustered network that controls focal adhesion signaling during muscle regeneration

city: Zurich

last: Krützfeldt

state: Zurich

address: Rämistrasse 100

department: Division of Endocrinology, Diabetes and Clinical Nutrition

country: Switzerland

institute: University Hospital Zurich

summary: Objective: Decreased muscle mass is a major contributor to age-related morbidity, and strategies to improve muscle regeneration during ageing are urgently needed. Our aim was to identify the subset of relevant microRNAs (miRNAs) that partake in critical aspects of muscle cell differentiation, irrespective of computational predictions, genomic clustering or differential expression of the miRNAs.  Methods: miRNA biogenesis was deleted in primary myoblasts using a tamoxifen-inducible CreLox system and combined with an add-back miRNA library screen. RNA-seq experiments, cellular signalling events, and glycogen synthesis, along with miRNA inhibitors, were performed in human primary myoblasts. Muscle regeneration in young and aged mice was assessed using the cardiotoxin (CTX) model.   Results: We identified a hierarchical non-clustered miRNA network consisting of highly (miR-29a), moderately (let-7) and mildly active (miR-125b, miR-199a, miR-221) miRNAs that cooperate by directly targeting members of the focal adhesion complex. Through RNA-seq experiments comparing single versus combinatorial inhibition of the miRNAs, we uncovered a fundamental feature of this network, that miRNA activity inversely correlates to miRNA cooperativity. During myoblast differentiation, combinatorial inhibition of the five miRNAs increased activation of focal adhesion kinase (FAK), AKT, and p38 mitogen-activated protein kinase (MAPK), and improved myotube formation and insulin-dependent glycogen synthesis. Moreover, antagonizing the miRNA network in vivo following CTX-induced muscle regeneration enhanced muscle mass and myofiber formation in young and aged mice.   Conclusion: Our results provide novel insights into the dynamics of miRNA cooperativity and identify a miRNA network as therapeutic target for impaired focal adhesion signalling and muscle regeneration during ageing.

overall_design: We performed genome-wide identification of differentially expressed genes and miRNA target regulation after single or combinatorial miRNA inhibition in human myotubes. Human myoblasts derived from 3 donors were treated with control antagomirs or antagomirs either against let-7, miR-29a, miR-125b, miR-199, miR-221 or against all miRNAs (ant-5x). Twenty-four hours after transfection differentiation was induced for two days and total RNA was isolated. Libraries were prepared using TruSeq Stranded mRNA Library Prep kit (Illumina) and samples were sequenced using NovaSeq 100bp single-end sequencing at the Functional Genomics Center Zurich.

first: Edlira

last: Luca

first: Angelika

last: Hartung

first: Sebastian

last: Mathes

first: Hubert

last: Rehrauer


title: Analysis of mRNA expression between irradiated and non-irradiated keloid-derived primary cells.

status: Public on Jul 11 2020

city: Suzhou

first: Shuyu

address: Ren Ai Road 199

institute: Suzhou University

summary: This study aims to compare mRNA expression between irradiated and non-irradiated keloid-derived primary cells  by RNA-Seq. In this study, keloid-derived primary cells that were isolated from patients, and then divided into three groups and each group had four repeats. The first group of cells was treated without radiation, the second group of cells were received 4 Gy delivered in 2-Gy fractions once per day over 2 days and the third group of cells were received 8 Gy delivered in 2-Gy fractions once per day over 4 days.The last two groups of cells were irradiated at a fixed rate of 1.15 Gy/min using an X-ray linear accelerator (Rad Source Technologies Inc., Suwanee, GA, USA). 24 hours post irradiation of the third group of cells, all keloid-derived primary cells were collected and subjected to mRNA expression analysis.

overall_design: Keloid-derived primary cells that were isolated from patients, and then divided into three groups and each group had four repeats. The first group of cells was treated without radiation, the second group of cells were received 4 Gy delivered in 2-Gy fractions once per day over 2 days and the third group of cells were received 8 Gy delivered in 2-Gy fractions once per day over 4 days.The last two groups of cells were irradiated at a fixed rate of 1.15 Gy/min using an X-ray linear accelerator (Rad Source Technologies Inc., Suwanee, GA, USA). 24 hours post irradiation of the third group of cells, all keloid-derived primary cells were collected and subjected to mRNA expression analysis.

first: Min

last: Hong


title: Transcriptomic profile of replicating NAFLD hepatocytes (from High-Fat High-Sucrose Diet - HFHS and Choline-Deficient High-Fat Diet - CDHFD).

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

institute: INSERM

summary:
C57Bl6/J male mice were put on different diets at 5 weeks of age, with a standard diet (SD) or a High-Fat High-Sucrose Diet (HFHS) or a Choline-Deficient High-Fat Diet (CDHFD) during 6 months. Primary hepatocytes cultures from 3 different models were synchronized in the cell cycle.
Transcriptomic analysis was perfomed at 48hours of culture when HFHS and CDHFD hepatocytes harbor replication stress.

overall_design: 3 groups (SD, HFHS and CDHFD) were analyzed with 3 mice per group

first: Romain

last: Donne

first: Chantal

last: Desdouets


title: Mutant Kras co-opts a progenitor-derived enhancer network to initiate pancreatic tumorigenesis [scATAC-seq]

first: Yi

last: He

address: 30 Shuangqing Rd, Haidian Qu, Beijing Shi, China

institute: Tsinghua university

summary: Oncogenes are highly specific in the cells they can transform, although the molecular basis for this is poorly understood. Inflammation often promotes tumorigenesis, and in the pancreas it promotes cellular plasticity and accelerates Kras-driven neoplasia. We demonstrate that plasticity is coupled to the emergence of transient progenitor cells that are readily transformed by KrasG12D. The progenitor state is linked to coordinate upregulation of proliferation genes through chromatin opening at nearby lineage-specific enhancers. Mutant Kras taps into this program by co-opting the normally transient enhancer elements, making them permanent and Kras-dependent in cancer. Mechanistically, co-option occurs through cooperation of Kras-driven transcription factors with the existing landscape of pancreatic lineage transcription factors, which are recruited to play a central role in driving the mutant Kras-dependent transcriptional program. These observations suggest that proliferation is controlled by tissue-specific enhancer networks that are tapped into by oncogenes, helping explain the lineage specificity of cancer drivers.

overall_design: Examination of chromatin accessiblity of PDAC tumor sample, para-tumor sample and normal sample from human pancreatic tissue.

first: Charles

last: David

first: Yong

last: Li


title: Comprehensive transcriptome analysis of human myofibroblasts with/without the JQ-1 treatment [mRNA]

city: Chiba

first: Yoshitoshi

last: Kasuya

address: 1-8-1 Inohana Chuo-ku

institute: Chiba Univ.

summary: Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease that normal parenchyma is progressively replaced by fibrotic foci comprised of myofibroblasts, active differentiated fibroblasts. IPF has an overall poor prognosis with median survival ranging from 2.5 to 3.5 years. The underlying disease mechanisms in IPF are largely unknown, and there is still no effective drug that prolongs survival of patients with IPF.  It has been known that JQ-1, a BET bromodomain inhibitor, prevents TGF-β-mediated fibroblast to myofibroblast differentiation. In this study, to obtain a better understanding of the molecular mechanisms underlying the effect of JQ-1 treatment on the dedifferentiation of established myofibroblasts, we performed comparative transcriptome analysis using the high-throughput RNA-seq. The CLC Genomic Workbench software was used to screen the differentially expressed transcripts. A total of 4,155 genes with a significantly differential expression in the JQ-1 treatment group as compared with the control group.

overall_design: mRNA profiles of cells were generated by RNA sequencing using the NextSeq 500 (Illumina).

first: Kenichi

last: Suzuki

first: Koichiro

last: Tatsumi