title: Differential DNA Methylation in the PFC across the transition from acute to chronic pain

status: Public on May 26 2020

city: Minneapolis

first: Laura

last: Stone

address: 420 Delaware Street SEMMC 294

institute: University of Minnesota

summary: We performed genome-wide bisulfite capture sequencing in prefrontal cortex in male mice at four timepoints (one day, two weeks, six months, and one year) post-neuropathic injury in order to track and observe dynamics of DNA methylation and epigenetic regulation in response to the development of chronic pain. We identified hundreds of differentially methylated CpGs and genes at FDR < 0.1 and differential methylation > 5%. PFC DNA methylation rapidly and robustly responds to neuropathic injury and genes display time point specific patterns of differential methylation.

overall_design: Comparison of DNA methylation between Sham PFC and SNI PFC at four time points

first: Lucas

last: Topham

first: Moshe

last: Szyf


title: Evaluation of drug escape mutant in Sendai virus

city: new york

first: satoshi

last: ikegame

state: new york

address: 1468 madison avenue, Annenbergbuilding 17-24

department: microbiology

country: USA

institute: Icahn school of medicine at Mount Sinai

summary: We report drug escape mutant of Sendai virus.

overall_design: 6 independent trial in Sendai virus

first: Satoshi

last: Ikegame

first: Robert

middle: M

last: Cox


title: Adropin stimulates proliferation and inhibits adrenocortical steroidogenesis via the TGF-beta mediated pathway in the human adrenal carcinoma (HAC15) cell line.

status: Public on May 19 2020

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

country: Poland

institute: Poznan University of Medical Science

summary:
Adropin is a multifunctional peptide hormone encoded by the ENHO (energy homeostasis associated) gene. It plays a role in mechanisms related to increased adiposity, insulin resistance, as well as glucose and lipid metabolism. The low adropin levels are strongly associated with obesity independent insulin resistance. On the other hand, overexpression or exogenous administration of adropin improves glucose homeostasis. The multidirectional, adropin-related effects associated with the regulation of metabolism in humans also appear to be attributable to the effects of this peptide on the activity of various elements of the endocrine system including adrenal cortex. Therefore, the main purpose of the present study was to investigate the effect of adropin on proliferation and secretory activity in the human HAC15 adrenal carcinoma cell line.
We also found that HAC15 cells treated with adropin presented significantly higher proliferation levels than untreated cells. Based on whole transcriptome study and research involving transforming growth factor (TGF)-β type I receptor kinase inhibitor we demonstrated that attenuation of steroidogenesis caused by adropin is mediated by the TGF-β signalling pathway likely to act through transactivation mechanism.

overall_design: HAC15 cell line (ATCC® CRL-3301TM, VA, USA) was cultured in a defined medium consisting of DMEM/F-12 without phenol red (Thermo Fisher Scientific, Waltham, MA, USA), 10% Cosmic Calf Serum (Hyclone, GE Healthcare, MA USA), 1% ITS + Premix (Corning, NY, USA), and 1% P/S (Merck Millipore, Darmstadt, Germany). The cells at low passages (p0-p1) underwent starvation in the DMEM/F-12 medium supplemented with 10% charcoal-stripped fetal bovine serum (FBS) (Thermo Fisher Scientific, MA, USA) and 1% P/S for 24h. Subsequently, the cells were treated with the following compounds: ACTH (Synacthen) 10-7 M (Basel, Switzerland), forskolin 25μM (Merck Millipore, Germany), and adropin 10-8 M (Bachem, Switzerland) for another 24h. The cells cultured in the medium with 10% charcoal-stripped FBS served as controls. Immediately after 24h of incubation, the cells and culture media were collected and stored at -80C for microarray study

first: Ewekina

last: Stelcer

first: Paulina

last: Milecka


title: Physical activity modulates macrophage phenotype in mammary tissue and inhibits tumor progression

status: Public on May 15 2020

city: Los Angeles

first: Donald

middle: M.

last: Lamkin

state: CA

address: 300 UCLA Medical Plaza, Room 3160

department: Semel Institute for Neuroscience

institute: UCLA

type: Expression profiling by high throughput sequencing

summary: We generated RNAseq results from the mammary tissues of mice from a 2 x 2 factorial design experiment (running wheels vs. control condition X clodronate liposomes vs. PBS liposomes) where EO771 mammary cancer cells had been engrafted in the mammary tissue for nascent tumor formation. RNAseq results were used to complete digital cytometry with the CIBERSORTx platform to analyze relative proportions of M1-like and M2-like macrophages in the mammary tissue.

overall_design: Total RNA was purified from mouse mammary tissues with engrafted EO771 cells from a 2 x 2 factorial design experiment: running wheels vs. control condition X clodronate liposomes vs. PBS liposomes. Control+PBS (n=6), Wheel+PBS (n=6), Control+Clodronate (n=5), Wheel+Clodronate (n=5). Mice used were 7-8 week-old female C57BL/6J mice (Jackson Laboratory) and were housed on an individually ventilated cage (IVC) rack in dual filter disposable cages (Innovive, Inc.), with corn cob bedding, nesting tissue, and ad libitum access to food and water on a 12:12 light:dark cycle at 22oC.  Mice were given access to an angled running wheel-hub apparatus (Fast-Trac Mouse Igloo®, Bio-Serve, Flemington, NJ) in each home cage for two weeks or only to a hub if control mice.  At the conclusion of the two-week period, the left 4th mammary fat pad was engrafted with 1 × 10^5 cells of the syngeneic mammary cancer cell line, EO771 (CH3 Biosystems, LLC), which had been transduced to express firefly luciferase. Mice were also injected intravenously with liposomes (Liposoma BV) at both 24 hours before and again at the time of tumor engraftment.  Mice continued to have wheel access for another 24 hours after engraftment before euthanasia for mammary tissue collection.  Each left 4th mammary tissue was dissected and lysed so that total RNA could be extracted (Qiagen RNeasy Mini Kit, #74104), cleared of contaminating DNA with on-column DNase digestion (Qiagen RNase-Free DNase Set, #79254), and quantified by spectrophotometry (NanoDrop ND-1000, Thermo Scientific).  Total RNA was converted to cDNA (Lexogen QuantSeq 3′FWD), sequenced using an Illumina HiSeq 4000 instrument in the UCLA Neuroscience Genomics Core Laboratory, and low-level sequencing data was mapped to the RefSeq mouse genome sequence and normalized to counts per million mapped reads (CPM).  All procedures were carried out under protocols approved by the Institutional Animal Use and Care Committee of the University of California, Los Angeles.


title: A Small-RNA-Mediated Feedback Loop Maintains Proper Levels of 22G-RNAs in C. elegans

status: Public on May 21 2020

city: Arlington

first: Alicia

middle: Kathryn

last: Rogers

state: Texas

address: 1225 W Mitchell Street

department: Department of Biology

institute: University of Texas at Arlington

type: Non-coding RNA profiling by high throughput sequencing

summary: ERI-6/7 is a negative regulator of exogenous RNAi, however the function of SOSI-1 has never previously been characterized. We noticed that expression of sosi-1 and eri-6/7 are mutually exclusive. Due to its genomic locus being nested within the eri-6 locus, we hypothesized that sosi-1 could be acting as a regulator of ERI-6/7 function by disrupting eri-6/7 expression upon sensing changes in the production of MUT-16-dependent 22G siRNAs. Our data confirms that expression of the sosi-1 mRNA is regulated by MUT-16-dependent 22G siRNAs. In addition, we show here that the expression of the eri-6 and eri-7 pre-mRNAs, and thus the eri-6/7 trans-spliced mRNA, are mis-regulated upon loss of sosi-1-targeting and eri-6[e-f]-targeting MUT-16-dependent 22G siRNAs, suggesting that sosi-1 and eri-6[e-f] act as a feedback sensor for small RNA function.

overall_design: 24 mRNA-seq libraries and 30 small RNA-seq libraries were generated and analyzed. Each genotype per condition were generated in triplicate.

middle: K

first: Carolyn

last: Phillips


title: Efficient generation and transcriptomic profiling of human iPSC-derived pulmonary neuroendocrine cells

status: Public on May 13 2020

first: Vasu

last: Punj

address: Biggy Street

institute: USC

summary: Expansion of pulmonary neuroendocrine cells (PNECs) is a pathological feature of many human lung diseases. Human PNECs are inherently difficult to study due to their rarity (<1% of total lung cells) and a lack of established protocols for their isolation. We used induced pluripotent stem cells (iPSCs) to generate induced PNECs (iPNECs) which express core PNEC markers, genes therby recapitulating known functions of primary PNECs. Single-cell RNA sequencing (scRNA-seq) of these iPNEC revealed a PNEC-associated gene expression profile that is concordant between iPNECs and human fetal PNECs. In conclusion, our model has the potential to provide an unlimited source of human iPNECs to explore PNEC pathophysiology associated with several lung diseases.

overall_design: Examination of 2 iPSC replicates for their differentiation to iPNEC.

first: Pooja

last: Hor

first: V

first: B

middle: A

last: Calvert

first: A

last: Castaldi

middle: J

last: Miller

first: G

last: Carraro

middle: R

last: Stripp

first: S

middle: L

last: Brody

first: J

last: Spence

last: Ichida

first: Amy

last: Ryan

first: Z

last: Borok


title: Quantitative Analysis of different NK cell types Transcriptomes

city: La Jolla

first: Benjamin

last: Goldenson

address: 2880 Torrey Pines Scenic Dr

institute: UCSD

summary: We compared transcriptome of different types of NK cells including obtained from Umbilical  Blood (UCB-NK) from 3 donors, both UCB56 NK cells that were isolated from the UCB unit as well as UCB34 NK cells that were differentiated from CD34+ cells, and derived from human iPSC (iPSC-NK), pre and post antigen presenting cell expansion. When comparing the similarity of the NK cells populations by the number of differentially expressed genes to iPSC NK cells, there were the pre and post expansion cells clustered together

overall_design: mRNA profiles of 4 different NK cell types from 3 donors and iPS NK cells were generated by deep sequencing, using Illumina Hi-seq 2000.

first: Huang

last: Zhu

first: Dan

last: Kaufman


title: Gene expression data from mouse salivary glands (wild type and Nfkbiz-deficient mice)

status: Public on May 27 2020

city: Seoul

first: Junho

last: Lee

state: Seoul

address: 88, Olympic-ro 43-gil, Songpa-gu, Seoul

department: Pathology

country: South Korea

institute: Asan

summary: We used microarrays to detail the global program of gene expression underlying identified distinct classes of up-regulated or down-regulated genes in salivary glands between Nfkbiz-/- and wild type mice.

overall_design: Total RNA samples obtained from the 20-week-old non-cohoused Nfkbiz+/+ and Nfkbiz-/- mice (n = 2 per group) were subjected to cDNA synthesis and labeling using the GeneChip™ WT PLUS Reagent Kit (ThermoFisher Scientific, Waltham, MA, USA) and then transcriptome analysis using the Affymetrix whole-transcript expression arrays (ThermoFisher Scientific) at Macrogen Inc. (Seoul, Korea).

first: Youngnim

last: Choi


title: single-cell RNA-seq profile of microglia under acute Csf1r inhibition and early repopulation in adult brain

status: Public on May 09 2020

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

summary: Microglia are the resident myeloid cell in the central nervous system (CNS). Like other terminally differentiated myeloid cells, microglia rely on Csf1r signaling for survival and maintenance. Surprisingly, a small subset of microglia in the murine brain can survive without Csf1r signaling, as shown in Csf1r KO mice as well as in mice that have been treated with Csf1r inhibitor PLX5622. The nature of such Csf1r independent microglial population has not been fully characterized. Here we applied single-cell RNA-seq to examine the remaining microglia in C57/BL6J mice that were treated with PLX5622 diet (1200 mg/kg, 14 days), which results >90% microglial removal.

overall_design: Mice were placed on PLX diet (1200 mg/kg) for 14 days to deplete microglia (D0). The early stage microglia repopulation (D2) group was switched to control diet (CD) for 2 days. Adult microgia from ctrl (untreated) and the treated mice were isolated by FACS using Cd11b antibody.

first: Lihong

last: Zhan

last: Fan


title: Epigenomic effect of talc particles on macrophages

status: Public on May 12 2020

city: Providence

first: Tania

last: Emi

state: RI

address: 593 Eddy St.

department: Rhode Island Hospital

institute: Brown University

type: Methylation profiling by high throughput sequencing

summary: Our objective was to investigate epigenomic and transcriptomic changes in J774 macrophages after incubation with talc and titanium dioxide particles. This dataset comprises the results of reduced representation bisulfite sequencing (RRBS) of the J774 cell DNA 24 hours after exposure to 10 ug/well of fine-sized talc or titanium dioxide particles in vitro with or without 2 ug/mL 17-b estradiol.

overall_design: Reduced representation bisulfite sequencing of genomic DNA extracted from J774 cells after talc and TiO2 (with/without estrogen) particle exposure, in triplicates.

first: Loreilys

last: Mejias-Rivera

first: Joselynn

last: Wallace

first: Ashok

last: Ragavendran

first: Alexey

last: Fedulov


title: High resolution genome-wide occupancy in Candida species using ChEC-seq

status: Public on May 08 2020

city: Québec

first: Faiza

last: Tebbji

address: 2705 Boulevard Laurier

country: Canada

institute: CHU Québec

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chromatin endogenous cleavage (ChEC) uses fusion of a protein of interest to micrococcal nuclease (MNase) to target calcium-dependent cleavage to specific genomic loci in vivo. Here we report the combination of ChEC with high-throughput sequencing (ChEC-seq) to determine genomic occupancy of the generalist transcription factor Nsi1 and the catalytic subunit of the SWI/SNF chromatin remodelling complex Snf2 in the opportunistic yeast Candida albicans. Time-based analysis of ChEC-seq data reveals two classes of sites for each transcriptional regulator, one exhibiting rapid cleavage during the first 5 min with robust consensus motifs and the second showing slow cleavage at largely unique sites with low-scoring motifs. The ChEC-seq procedure described here will allow a high-resolution genomic location definition which will enable a better understanding of transcriptional regulatory circuits that govern fungal fitness and drug resistance in these medically important fungi.

overall_design: We adapted ChEC to a genome-wide sequencing readout (ChEC-seq) described in S. cerevisae to map the genome-wide distributions of the C. albicans transcription factors Snf2 and Nsi1 without the limitations associated with ChIP-based methods.

first: Inès

last: Khemiri

first: Adnane

last: Sellam


title: Impact of drought and plant litter chemistry on microbial gene expression

status: Public on May 01 2020

city: Aberdeen

first: Ashish

last: Malik

address: St Machar drive

country: United Kingdom

institute: University of Aberdeen

summary: Drought represents a significant stress to microorganisms and is known to reduce microbial activity and organic matter decomposition in Mediterranean ecosystems. However, we lack a detailed understanding of the drought stress response of microbial decomposers. Here we present metatranscriptomic data on the physiological response of in situ microbial communities on plant litter to long-term drought in Californian grass and shrub ecosystems.

overall_design: Litter was collected in summer on 30 August 2017 from all four replicated plots within a treatment and homogenized by hand-mixing. Litter bags were made by placing 6 g dry litter mass into 15 cm x15 cm bags made from 1 mm mesh window screen. Bags were deployed on 12 September 2017. An in-situ pulse wetting was performed on 30 November 2017 to simulate a discrete rainstorm of ~13 mm using previously collected rainwater. Litter bags were collected before wetting (Sampling 1) and another batch of bags was collected the following day (Sampling 2). There was no precipitation in the following days and therefore the litter dried to pre-wetting moisture levels. We collected another batch 12 days after wetting (Sampling 3). Sixteen litter bags were sampled at each time point (2 vegetation types  x 2 precipitation treatments x 4 replicates). Retrieved litter bags were immediately transported to the lab at room temperature.


title: Antigen-specific memory and naïve CD4+ T cells following secondary Chlamydia trachomatis infection

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Memory antigen-specific CD4+ T cells against Chlamydia trachomatis are necessary for protection against secondary genital tract infection. While it is known that naïve antigen-specific CD4+ T cells can traffic to the genital tract in an antigen-specific manner, these T cells are not protective during primary infection. Here, we sought to compare the differences between memory and naïve antigen-specific CD4+ T cells in the same mouse following secondary infection using transgenic CD4+ T cells (NR1 T cells). Using RNA sequencing, we found that there were subtle but distinct differences between these two T cell populations. Naïve NR1 T cells significantly upregulated cell cycle genes and were more proliferative than memory NR1 T cells in the draining lymph node. In contrast, memory NR1 T cells were more activated than naïve NR1 T cells and were enriched in the genital tract. Together, our data provide insight into the differences between memory and naïve antigen-specific CD4+ T cells during C. trachomatis infection.

overall_design: Two samples each in triplicate

first: Jennifer

middle: D

last: Helble

first: Alexander

middle: O

last: Mann

first: Michael

middle: N

last: Starnbach


title: DNA methylation covariation in human whole blood and sperm

status: Public on May 03 2020

city: London

first: Sarah

last: Marzi

address: Du Cane Road

institute: Imperial College London

type: Methylation profiling by genome tiling array

summary: Epidemiological studies in humans suggest that acquired paternal traits, such as obesity, are associated with a higher risk of fathering small for gestational age offspring. Studies in non-human mammals suggest that such associations could be mediated by DNA methylation changes in spermatozoa that influence offspring development in utero. Human obesity is associated with differential DNA methylation in peripheral blood. It is unclear, however, whether this differential DNA methylation is reflected in less readily available tissues such as spermatozoa. In this study, we profiled genome-wide DNA methylation with the Infinium MethylationEPIC array in matched samples of human blood and sperm from lean (discovery n = 47; replication n = 21) and obese (n = 22) healthy males of proven fertility. To characterize sperm-specific DNA methylation signatures, we compared spermatozoal DNA methylation data to that of nearly 6,000 somatic tissue samples available on the Gene Expression Omnibus database. We studied covariation patterns between whole blood and sperm and investigated consistent obesity-associated DNA methylation differences.

overall_design: Matched whole blood and sperm DNA methylation samples were collected from 47 lean, healthy men. Two replication cohorts included matched whole blood and sperm DNA methylation samples from 21 lean men and 22 obese men, respectively. The samples were analyzed for differences in DNA methylation between whole blood and sperm (paired t-test), covariation between the two tissues (Pearson's correlation test) and obesity associations (linear models in each of the tissues; linear mixed effects model across both tissues and all three cohorts)


title: Sir2 and Hst1 ChIP-Seq in Saccharomyces cerevisiae

city: Houston

first: Lisha

last: Zhu

state: TX

address: 7000 fannin st

institute: UT Health Science Center at Houston

summary: Chromatin Immunoprecipitation followed by high throughput sequencing to identify the location of Sir2 and Hst1 genomic enrichment.

overall_design: This data represents two technical replicates for each IP sample and the mock IP (both Sir2-HA and Hst1-HA). There is also 1 genomic input sample.

first: Kristen

last: Humphrey

first: Tao

last: Liu

first: Laura

last: Rusche


title: RNA-seq in WT and sir2∆ K. lactis yeast strains

summary: Evaluation of the differential expression of mRNA between WT and sir2∆in K. lactis yeast strains.

overall_design: There are two technical replicates of WT mRNA (2 samples) and two technical replicates of two biological isolates of sir2∆ mRNA (4 samples)


title: Impact of maturation and growth temperature on transcription profiles of Penicillium roqueforti conidia

status: Public on Apr 24 2020

city: Utrecht

first: Maarten

last: Punt

state: Nederland

address: Padualaan 8

country: Netherlands

institute: Utrecht University

summary:
Purpose: The goal of this study is to compare differences between Penicillium roqueforti conidia from various conditions shown to affect heat-resistance to identify genes possibly related to heat-resistance using RNA-seq.
Methods: mRNA from Penicillium roqueforti conidia produced at different temperatures (15C, 25C or 30C) and different cultivation times (3, 5, 7 or 10 days) was extracted, in triplicate, and sequenced with Illumina  NextSeq500. The sequence reads that passed quality filters were analyzed using Hisat2 followed by Cufflinks.
Results: we mapped about 19 million sequence reads per sample to the Penicillium roqueforti genome (build LCP96 04111) and identified 9723 transcripts in the conidia. Data analysis revealed a subset of 33 genes showing increased expression in culture conditions that increase heat-resistance.
Conclusions: Our study generated insight into multiple genes that are likely involved in the heat-resistance of Penicillium roqueforti.

overall_design: mRNA profiles of conidia from 3,5,7, and 10 day old Penicillium roqueforti cultures grown at 25C, and  profiles of conidia from 7 day old cultures grown at 15C and 30C were generated, in triplicate, with deep sequencing using Illumina NextSeq 500.

first: Tom

last: van den Brule

first: Wieke

last: Teertstra

first: Jan

last: Dijksterhuis

first: Heidy

last: den Besten

first: Robin

last: Ohm

first: Han

last: Wösten


title: RNA-seq expression analysis of E.coli in rich-M9 medium for HGT study

status: Public on Apr 16 2020

city: Liverpool

first: Jonathan

middle: P

last: Bollback

state: Merseyside

address: Crown Street, Biosciences Building, Room 305

department: Functional and Comparative Genomics

institute: University of Liverpool

summary: We have estimated the fitness effects of horizontally transferred Salmonella genes to E.coli. To better understand the role of protein-protein interactions, we want to identify the expression levels of known interaction partners of the transferred genes.

overall_design: Gene expression of E.coli carrying the plasmid with an mCherry gene under the control of the pLtet0-1 promoter, after 1 hour of induction with 5ng/mL Anhydrotetracycline, grown in rich M9 medium until OD 600: 0.12, in deep well plates, each well containing 1mL. Total RNA is isolated from the total volume of 16mL.

first: Hande

last: Kirit


title: Discovering the Molecular Determinants of Phaeobacter inhibens susceptibility to Phaeobacter phage MD18

status: Public on Apr 12 2020

first: Guillaume

last: Urtecho

address: 607 Charles E. Young Drive

department: Molecular Biology

institute: University of California, Los Angeles

summary: We identify genetic determinants of Phaeobacter inhibens susceptibility to Phaeobacter phage MD18

overall_design: We screen Phaeobacter phage MD18 against a library of Phaeobacter inhibens barcoded transposon insertion mutants

first: Danielle

middle: E

last: Campbell


title: The DNA Methylation Landscape of the Human Cancer Organoids Available at the American Type Culture Collection

status: Public on Mar 30 2020

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: Josep Carreras Leukaemia Research Institute (IJC)

summary: Study of the DNA methylation profile of different human cancer organoids.

overall_design: 25 organoid gDNA samples from ATCC were analyzed.

first: M

first: R

last: Joshi


title: ChIP-chip analysis of Sir2 and Orc1 in Kluyveromyces lactis

first: Lisha

last: Zhu

type: Genome binding/occupancy profiling by genome tiling array

summary: Chromatin Immunoprecipitation followed by microarray analysis to identify the location of Sir2 and Orc1 genomic enrichment.

overall_design: Sir2-HA was immunoprecipitated from strains LRY2021 or LRY2022.  For LRY2021, the IP sample was labeled with Cy5 and the input was labeled with Cy3.  For LRY2022, the dyes were swapped.  Labeled DNA was hybridized to a custom ChIP-on-Chip 2x105K microarray (Agilent G4498A), designed with 102,839 60-nucleotide probes tiled across the K. lactis genome spaced approximately every 100 bp (AMADID 018357).

first: Meleah

last: Hickman


title: Differences in gynecologic tumor development in Amhr2-Cre mice with KRASG12D or KRASG12V mutations

status: Public on Apr 01 2020

first: Kwong-Kwok

last: Wong

address: T4-3900, 1515 Holcombe Boulevard

department: Gynecologic Oncology and Reproductive Medicine

institute: UT M. D. Anderson Cancer Center

summary: We report the RNAseq data from uterine tissues obtained from mice that over-express KRAS-G12D or KRAS-G12V oncogenes in a Ahmr2-Cre Pten null genetic background.

overall_design: The gene expression profiles of mice expressing KRAS-G12D or KRAS-G12V are compared to mice without KRAS mutations in the same genetic Ahmr2-Cre Pten null background.


title: Modeling Human Cytomegalovirus-Induced Microcephaly in Human iPSC-derived Brain Organoids

status: Public on Mar 25 2020

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: We show that HCMV infection of human induced pluripotent stem cell (hiPSC)-derived brain organoids can recapitulate severe clinical manifestations such as microcephaly. We demonstrate that infection of hiPSC-derived brain organoids by the “clinical-like” HCMV strain TB40/E results in substantially reduced brain organoid growth, impaired formation of cortical layers, abnormal calcium signaling, and disrupted neural network. Accordingly, RNA-seq analysis revealed that genes down-regulated in TB40/E-infected brain organoids include those involved in neural development and calcium signaling. Moreover, we show that the impeded brain organoid development and abnormal neural network caused by TB40/E infection can be prevented by neutralizing antibodies (NAbs) that recognize different epitopes of the HCMV envelope pentamer complex (PC), a major target of HCMV-specific humoral immunity. These results demonstrate in a three-dimensional human cellular biosystem that HCMV can cause severe brain malformation and disrupt calcium signaling and neural network activity. This study also provides insights into the potential capacity of NAbs to mitigate brain defects resulted from congenital HCMV infection.

overall_design: Examine the differentiation gene expression between iPSC-derived brain organoid infected with CMV and mock infection

first: Guoqiang

last: Sun

first: Flavia

last: Chiuppesi

first: Xianwei

last: Chen


title: Single-cell RNA sequencing of murine islets shows high cellular complexity at all stages of autoimmune diabetes

status: Public on Mar 27 2020

city: St. Louis

first: Pavel

last: Zakharov

state: MO

address: 660 S Euclid Ave Box 8118

department: Pathology and Immunology

institute: Wash.Univ in St. Louis

summary: Tissue-specific autoimmune diseases are driven by activation of diverse immune cells in the target organs. However, the molecular signatures of immune cell populations over time in an autoimmune process remain poorly defined. Using single-cell RNA sequencing, we performed an unbiased examination of diverse islet-infiltrating cells during autoimmune diabetes in the nonobese diabetic mouse. The data revealed a landscape of transcriptional heterogeneity across the lymphoid and myeloid compartments. Memory CD4 and cytotoxic CD8 T cells appeared early in islets, accompanied by regulatory cells with distinct phenotypes. Surprisingly, we observed a dramatic remodeling in the islet microenvironment, in which the resident macrophages underwent a stepwise activation program. This process resulted in polarization of the macrophage subpopulations into a terminal proinflammatory state. This study provides a single-cell atlas defining the staging of autoimmune diabetes and reveals that diabetic autoimmunity is driven by transcriptionally distinct cell populations specialized in divergent biological functions.

overall_design: Transcriptional analysis of islet cells as a function of autoimmune diabetes progression using whole population (bulk) and single-cell RNASeq


title: A single cell analysis of the molecular lineage of chordate embryogenesis

city: Shanghai

first: Tengjiao

last: Zhang

state: Shanghai

address: 1239 Siping Road

department: School of life science and technology

country: China

institute: Tongji University

summary: Progressive unfolding of gene expression cascades underlies diverse embryonic lineage development. Here, we report a single-cell RNA sequencing analysis of the complete and invariant embryonic cell lineage of the tunicate Ciona savignyi from fertilization to the onset of gastrulation. We reconstructed a developmental landscape of 47 cell types over eight cell cycles in the wild-type embryo and identified eight fate transformations upon fibroblast growth factor (FGF) inhibition. For most FGF-dependent asymmetric cell divisions, the bipotent mother cell displays the gene signature of the default daughter fate. In convergent differentiation of the two notochord lineages, we identified additional gene pathways parallel to the master regulator T/Brachyury. Last, we showed that the defined Ciona cell types can be matched to E6.5-E8.5 stage mouse cell types and display conserved expression of limited number of transcription factors. This study provides a high-resolution single-cell dataset to understand chordate early embryogenesis and cell lineage differentiation.

overall_design: we dissociated multiple embryos at each stage, collected essentially every cell from each embryo and generated single-cell transcriptome using a modified Smart2 protocol. In total, we obtained 745 single cell expression profiles with 2-8 embryos at each stage and detected on average >5,000 genes and 48,340 of UMIs per cell

first: Yichi

last: Xu

first: Weiyang

last: Shi

first: Zhirong

last: Bao


summary: Whole population RNASeq of pancreatic islet macrophages during autoimmune diabetes progression.

overall_design: RNASeq

first: Hao

last: Hu

first: Xiaoxiao

last: Wan

first: Emil

last: Unanue


title: Transcriptomic analysis of CIC and ATXN1L in normal human astrocytes

status: Public on Mar 31 2020

city: Vancouver

first: Derek

state: British Columbia

address: 675 W 10th Ave

department: Molecular Oncology

institute: University of British Columbia

summary: Aberrations in Capicua (CIC) have recently been implicated as a negative prognostic factor in a multitude of cancer types through activation of the MAPK signalling cascade and derepression of oncogenic ETS transcription factors. The Ataxin-family protein ATXN1L has previously been reported to interact with CIC in developmental and disease contexts to facilitate the repression of CIC target genes. To further investigate this relationship, we performed functional in vitro studies utilizing ATXN1LKO and CICKO human cell lines and characterized a reciprocal functional relationship between CIC and ATXN1L.

overall_design: 3 biological replicates for each sample, two monoclonal knockouts per knockout condition. The parental line is a polyclonal normal human astrocyte immortalized with E6/E7 and overexpressing wildtype IDH1. CIC knockout monoclonal lines are labeled A2 and H9. ATXN1L knockout monoclonal lines are labeled B82 and B16

first: Stephen

last: Yip


title: Defective minor spliceosomes induce SMA-associated phenotypes through sensitive intron-containing neural genes in Drosophila

first: Liang

last: Li

address: 300 Fenglin Road

institute: University of Chinese Academy of Sciences

summary: The minor spliceosome is evolutionarily conserved in higher eukaryotes, but its biological significance remains poorly understood. Here, by precise CRISPR/Cas9-mediated disruption of the U12 and U6atac snRNAs, we report that a defective minor spliceosome is responsible for spinal muscular atrophy (SMA) associated phenotypes in Drosophila. Using a newly developed bioinformatic approach, we identified a large set of minor spliceosome-sensitive splicing events and demonstrate that three sensitive intron-containing neural genes, Pcyt2, Zmynd10, and Fas3, directly contribute to disease development as evidenced by the ability of their cDNAs to rescue the SMA-associated phenotypes in muscle development, neuromuscular junctions, and locomotion. Interestingly, many splice sites in sensitive introns are recognizable by both minor and major spliceosomes, suggesting a new mechanism of splicing regulation through competition between minor and major spliceosomes. These findings reveal a vital contribution of the minor spliceosome to SMA and to regulated splicing in animals.

overall_design: Detecting RNA levels in SMN mutation and two minor snRNAs mutation in Larva L3.

first: Yong-Zhen


title: Extensive 5'-Surveillance Guards Against Non-Canonical NAD-Caps of Nuclear mRNAs in Yeast

status: Public on Apr 28 2020

city: Heidelberg

first: Yaqing

state: baden württemberg

address: Im Neuenheimer Feld 364

department: Institute of Pharmacy and Molecular Biotechnology

country: Germany

institute: Heidelberg University

summary: The ubiquitous redox coenzyme nicotinamide adenine dinucleotide (NAD) acts as a noncanonical cap structure on prokaryotic and eukaryotic ribonucleic acids. Here we find that in budding yeast, NAD-RNAs are abundant (>1400 species), short (<170 nt), and mostly correspond to mRNA 5′-ends. The modification percentage of transcripts is low (<5%). NAD incorporation occurs mainly during transcription initiation by RNA polymerase II, which uses distinct promoters with a YAAG core motif for this purpose. Most NAD-RNAs are 3′-truncated. At least three decapping enzymes, Rai1, Dxo1, and Npy1, guard against NAD-RNA at different cellular locations, targeting overlapping transcript populations. NAD-mRNAs are not translatable in vitro. Our work indicates that in budding yeast, most of the NAD incorporation into RNA seems to be disadvantageous to the cell, which has evolved a diverse surveillance machinery to prematurely terminate, decap and reject NAD-RNAs.

overall_design:
NAD-RNA and All-cap-RNA profiling in wild type (WT) and mutant deletion of Npy1(n)/Dxo1(d)/Rai1(r) yeast strains.

Please note that [1] each *_merge_genome.wig file was generated from three replicates and is linked to the corresponding rep1 sample records [2] the rawHits*.txt and Stat*.txt data was generated from multiple samples as indicated in the corresponding sample description field and are linked as Series supplementary files.


title: Alteration of genome folding via engineered transposon insertion [Target-enriched sequencing]

status: Public on Mar 14 2020

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

summary: Mammalian chromosomes are partitioned into contact domains that can be conserved as functional units in evolution. Disruptions of domains can result from perturbed CTCF, cohesin, or chromosomal rearrangements. However, to what extent domains can be created de novo has not been explored in depth. Here, using a gain-of-function approach leveraging genome editing and Hi-C, we examined whether, and how, a putative boundary element can function to organize de novo domains in the context of multiple ectopic insertion sites. We subsequently dissected the distinct roles of the CTCF binding site and the transcription start site within the insertion element in changing genome folding.

overall_design: Using a transposon-based approach, we inserted a 2 kb DNA fragment, which resides within a tissue-invariant domain boundary, into the genomes of near-haploid HAP1 cells. Following transposition, we established clonal lines and prioritized Clones 21 (C21) and 25 (C25), which contained ten and six insertions, respectively, across a total of 11 chromosomes. We then performed in situ Hi-C on edited clones and unedited parental (WT) cells to characterize how the insertion of a boundary-associated DNA fragment shapes human genome architecture. Furthermore, we carried out a series of CRISPR-based editing experiments to dissect how the TSS and the CTCF binding site within the insertion element contributes to new domain formation. Additionally, we used CRISPR to delete the endogenous 2 kb element and characterized its function at its endogenous boundary. In addition to Hi-C, we performed Capture-C, ChIP-seq (CTCF, Rad21, and H3K27Ac), and RNA-seq to further characterize the structural changes resulting from each round of genome editing experiments.

first: Di

first: Peng

last: Huang

first: Sharma

last: Malini

first: Cheryl

last: Keller

first: Belinda

last: Giardine

first: Haoyue

first: Thomas

middle: G

last: Gilgenast

first: Jennifer

last: Phillips-Cremins

middle: C

first: Gerd

last: Blobel


title: Alteration of genome folding via engineered transposon insertion [H3K27Ac ChIP-seq]

last: Zhang


title: miRNA expression in cerebrospinal fluid with moyamoya disease

status: Public on Apr 03 2020

city: Guangzhou

first: Gang

last: Wang

state: Guangdong

address: 1023 Guangzhou Avenue North

department: Neurosurgery

institute: Nanfang Hospital of Southern Medical University

summary: We performed microarray analysis to determine the expression profiles of miRNAs in cerebrospinal fluid with moyamoya disease

overall_design: We obtained cerebrospinal fluid by lumbar puncture, and performed microarray analysis to identify differentially expressed miRNAs in normal and moyamoya patients.

first: Wang

last: Gang

first: Lv

last: Xiaoming


title: RNA-seq of two early-maturing rapeseed varieties treated with different cold stress

status: Public on Mar 19 2020

city: Changsha

first: Xin

last: He

state: Hunan

address: No. 1 Nongda Road, Furong district, Changsha, China

institute: Hunan Agricultural University

summary: Oil rapeseed (Brassica napus L.) is a typical winter biennial plant, with high cold tolerance during vegetative stage. In recent years, more and more early-maturing rapeseed varieties were planted across China. Unfortunately, the early-maturing rapeseed varieties with low cold tolerance have higher risk of freeze injury in cold winter and spring. Little is known about the molecular mechanisms for coping with different low-temperature stress conditions in rapeseed. In this study, we investigated 47,328 differentially expressed genes (DEGs) of two early-maturing rapeseed varieties with different cold tolerance treated with cold shock at chilling (4°C) and freezing (−4°C) temperatures, as well as chilling and freezing stress following cold acclimation or control conditions. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that two conserved (the primary metabolism and plant hormone signal transduction) and two novel (plant-pathogen interaction pathway and circadian rhythms pathway) signaling pathways were significantly enriched with differentially-expressed transcripts. Our results provided a foundation for understanding the low-temperature stress response mechanisms of rapeseed. We also propose new ideas and candidate genes for genetic improvement of rapeseed tolerance to cold stresses.

overall_design: Examination of 36 leaves samples (3 biological replications) of two early-maturing rapeseed varieties (HX17 and HX58) treated with cold shock at chilling (4°C) and freezing (−4°C) temperatures, as well as chilling and freezing stress following cold acclimation or control conditions.

first: Wei

last: Hua


title: Recurring urothelial carcinomas show genomic rearrangements incompatible with a direct relationship, implications for tumor development.

status: Public on Mar 13 2020

city: Lund

first: Nour-al-dain

last: Marzouka

address: Scheelevägen 2

department: Department of Clinical Sciences

country: Sweden

institute: Lund University

summary:
We made use of the fact that patients with non-muscle invasive tumors show frequent local recurrences and multiple tumors to study re-initiation of tumor growth from the same urothelium. By extensive genomic analyses we show that tumors from the same patient are clonal. We show that gross genomic chromosomal aberrations may appear abruptly and disappear with no transitional stages being observed. By analysis of incompatible changes i.e., genomic alterations that cannot be reversed, we show that almost all tumors from a single patient show such changes, thus the tumors cannot have originated from each other. As recurrent tumors share both genomic alterations and driver gene mutations, these must have been present in the histologically normal urothelium in periods with no tumor growth. We present a model that includes a growing and genomically evolving field of urothelial cells that occasionally, and locally, produce bursts of cellular growth leading to overt tumors.
This gene expression data was used to check the molecular subtypes based on Lund taxonomy (LundTax) in the recurring urothelial carcinomas.

overall_design: Total RNA from fresh-frozen resection samples of urothelial carcinomas was hybridized to the Illumina HumanHT-12 V3.0/V4.0 expression beadchip arrays (Illumina Inc) at the SCIBLU Genomics Centre at Lund University Sweden (http://www.lth.se/sciblu).

first: David

last: Lindgren

first: Pontus

last: Eriksson

first: Gottfrid

last: Sjödahl

first: Carina

last: Bernardo

first: Fredrik

last: Liedberg

first: Håkan

last: Axelson

first: Mattias

last: Höglund


title: Alteration of genome folding via engineered transposon insertion [CaptureC]

first: Ross

last: Hardison

first: Di

first: Peng

last: Huang

first: Sharma

last: Malini

first: Cheryl

last: Keller

first: Belinda

last: Giardine

first: Haoyue

last: Gilgenast


title: Alteration of genome folding via engineered transposon insertion [RNA-seq]

last: Zhang

first: Thomas

first: Jennifer

last: Phillips-Cremins

first: Gerd

last: Blobel


title: Evaluation of Eribulin Combined with Irinotecan for Treatment of Pediatric Cancer Xenografts

status: Public on Mar 10 2020

city: San Antonio

first: Yidong

last: Chen

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: Eribulin, irinotecan, and the combination were studied in ES4 xenograft model. RNAs from xenograft tumors were harvested at 24h and 144h after single agent or combination treatment to analyze gene expression.

overall_design: Gene expression profiles were generated using RNA-seq with 3 replicates at each time point (3 tumors from 3 separate mice) and 3 control samples (no treatment).

first: Andrew

last: Robles

first: Raushan

middle: T

last: Kurmasheva

first: Abhik

last: Bandyopadhyay

first: Doris

last: Phelps

first: Stephen

last: Erickson

first: Zhao

last: Lai

first: Dias

last: Kurmashev

first: Malcom

last: Smith

first: Peter

last: Houghton


title: RNAi pathways repress reprogramming of C. elegans germ cells during heat stress

status: Public on Mar 06 2020

city: Arlington

first: Alicia

last: Rogers

address: 1225 W Mitchell Street

department: Department of Biology

institute: University of Texas at Arlington

summary: Repression of cellular reprogramming in germ cells is critical to maintaining cell fate and fertility. When germ cells mis-express somatic genes they can be directly converted into other cell types, resulting in loss of totipotency and reproductive potential. Here we show that RNAi pathways play a key role in maintaining germline gene expression and totipotency after heat stress. By examining transcriptional changes that occur in mut-16 mutants, that lack a key protein in the RNAi pathway, at elevated temperatures we found that soma-specific genes are mis-expressed in germ cells. This trend was also observed in hrde-1 mutants, which fail to direct transcriptional silencing of RNAi-targeted genes. These findings indicate that the RNAi pathway plays a key role in preventing aberrant expression of somatic genes in the germline during heat stress. This regulation likely occurs in part through the maintenance of germline chromatin by the nuclear RNAi pathway.

overall_design: 12 mRNA-seq libraries, 12 small RNA-seq, and 12 ATAC-seq libraries were generated and analyzed. Each genotype per condition were generated in triplicate.

first: Carolyn

last: Phillips


title: Alteration of genome folding via engineered transposon insertion

first: Ross

last: Hardison

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

overall_design: Refer to individual Series


title: Longitudinal multi-omics reveals subset-specific mechanisms underlying irritable bowel syndrome

city: Rochester

first: Xiaojia

last: Tang

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

summary: The gut microbiome has been implicated in multiple human chronic gastrointestinal (GI) disorders. Determining its mechanistic role in disease pathogenesis has been difficult due to the apparent disconnect between animal and human studies and a lack of an integrated multi-omics view in the context of disease-specific physiological changes. We integrated longitudinal multi-omics data from the gut microbiome, metabolome, host epigenome and transcriptome in the context of irritable bowel syndrome (IBS) host physiology. We identified IBS subtype-specific and symptom-related variation in microbial composition and function. A subset of identified changes in microbial metabolites correspond to host physiological mechanisms that are relevant to IBS. By integrating multiple data layers, we identified purine metabolism as a novel host-microbial metabolic pathway in IBS with translational potential. Our study highlights the importance of longitudinal sampling and integrating complementary multi-omics data to identify functional mechanisms that can serve as therapeutic targets in a comprehensive treatment strategy for chronic GI diseases.

overall_design: We performed a longitudinal multi-omics study in humans, in an attempt to elucidate mechanistic roles for the gut microbiome in the pathophysiology of IBS. Healthy subjects and IBS-C and IBS-D patients between 18-65 years old who expressed interest were invited to undergo screening to assess eligibility. Participants were given the option of undergoing two flexible sigmoidoscopies. All IBS-C and IBS-D subjects fulfilled Rome III criteria. Recruitment of healthy subjects was matched with IBS subjects for age, sex and BMI.

first: Purna

last: Kashyap


title: STAT3 in the dorsal raphe gates behavioural reactivity and regulates gene networks associated with psychopathology

status: Public on Feb 29 2020

city: Vienna

first: Sonali

middle: N.

last: Reisinger

state: Vienna

address: Schwarzspanierstraße 17A

department: Center for Physiology and Pharmacology

country: Austria

institute: Medical University of Vienna

summary: The signal transducer and activator of transcription 3 (STAT3) signalling pathway is activated through phosphorylation by Janus kinases in response to a diverse set of immunogenic and non-immunogenic triggers. Several distinct lines of evidence propose an intricate involvement of STAT3 in neural function relevant to behaviour in health and disease. However, in part due to the pleiotropic effects resulting from its DNA binding activity and the consequent regulation of expression of a variety of genes with context-dependent cellular consequences, the precise nature of STAT3 involvement in the neural mechanisms underlying psychopathology remains incompletely understood. Here, we focussed on the midbrain serotonergic system, a central hub for the regulation of emotions, to examine the relevance of STAT3 signalling for emotional behaviour in mice by selectively knocking down raphe STAT3 expression using germline genetic (STAT3 KO) and viral-mediated approaches. Mice locally lacking STAT3 presented with reduced negative behavioural reactivity and a blunted response to the sensitising effects of amphetamine, alongside alterations in midbrain neuronal firing activity of serotonergic neurons and transcriptional control of gene networks relevant for neuropsychiatric disorders. Viral knockdown of dorsal raphe (DR) STAT3 phenocopied the behavioural alterations of STAT3 KO mice, excluding a developmentally determined effect and suggesting that disruption of STAT3 signalling in the DR of adult mice is sufficient for the manifestation of behavioural traits relevant to psychopathology.   Collectively, these results suggest DR STAT3 as a molecular gate for the control of behavioural reactivity, constituting a mechanistic link between the immune system, serotonergic neurotransmission and psychopathology.

overall_design: We aimed to study the alterations in gene expression in the dorsal raphe of mice lacking the transcription factor STAT3 in serotonergic cells by high-throughput sequencing of the midbrain dorsal raphe.

first: Spyros

last: Sideromenos

first: Orsolya

last: Horvath

first: Sophia

last: Derdak

first: Ana

last: Cicvaric

first: Francisco

last: Monje

first: Martin

last: Bilban

last: Häring

first: Micaela

last: Glat

first: Daniela

last: Pollak


title: Transcriptomic analysis of human astrocytes in vitro reveals hypoxia-induced mitochondrial dysfunction, modulation of metabolism and dysregulation of the immune response

status: Public on Feb 26 2020

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

institute: University of Sheffield

summary:
Changes in the transcriptomic profile of the Sciencell human astrocytes, after hypoxia treatment were compared to control cells receiving no treatment, to identify differentially expressed genes and pathways.
This study is to understand how hypoxia affects astrocytes and how this might reflect changes induced in circumstances such as ischaemia.

overall_design: The aim of this study was to carry out gene expression profiling of human astrocytes in response to hypoxia. It is thought that this may elucidate pathological processes that can be manipulated through therapeutic intervention to ultimately prevent neurodegeneration. Therefore, the current study performed a detailed characterization of the astrocyte gene expression profile in response to hypoxia in vitro, extending on previous reports and identifying novel candidate gene expression changes.

first: Scott

last: Allen

first: Rajpinder

middle: S

last: Seehra

first: Jessica

last: Bates

first: Claire

last: Garwood

first: Martyna

middle: M

last: Matuszyk

first: Stephen

middle: B

last: Wharton

first: Julie

last: Simpson


title: Comparative transcriptomics and co-expression networks reveal tissue- and genotype-specific responses to reproductive-stage drought stress in rice (Oryza sativa L.)

status: Public on Feb 25 2020

city: Los Banos

first: Jeshurun Asher

middle: Marayag

last: Tarun

state: Laguna

address: Pili Drive

department: Plant Breeding

country: Philippines

institute: International Rice Research Institute


title: Comparative transcriptomics and co-expression networks reveal tissue- and genotype-specific responses to reproductive-stage drought stress in rice (Oryza sativa L.) [flag-leaf]

summary: Purpose: The goal of the study is to compare the transcriptomic differences of the flag-leaf tissue at the reproductive-stage of the Introgression Line (IR 96321-1447-165-B-3-1-2), which is drought-tolerant, to Swarna (recipient parent), which is drought-sensitive.

overall_design: Flag-leaf mRNA profiles 2x2 factorial experiment under control and drought stress condition at the reproductive-stage of IL (drought-tolerant) and Swarna (drought-sensitive) were generated by deep sequencing with four independent biological replicates of each genotype under each conditions using Illumina HiSeq 4000.

first: Jeshurun

middle: A

first: Tobias

last: Kretzschmar


title: Gene expression profiling of long noncoding RNAs in myelodysplastic syndromes

status: Public on Feb 22 2020

city: Prague 2

first: Michaela

last: Dostalova Merkerova

address: U nemocnice 1

department: Department of Genomics

country: Czech Republic

institute: Institute of Hematology and Blood Transfusion

summary: Myelodysplastic syndromes (MDS) present a wide range of hematopoietic stem cell disorders with a tendency to evolve into acute leukemia. Long noncoding RNAs (lncRNAs) play multiple roles in hematopoiesis, contributing to the pathogenesis of hematologic malignancies and representing a new class of biomarkers and therapeutic targets. We aimed to characterize lncRNAs deregulated in MDS that may function in the disease pathogenesis and those that could serve as novel potential biomarkers of the disease. We performed a microarray expression profiling of lncRNAs and protein-coding genes (PCGs) in CD34+ bone marrow cells of MDS patients. Expression profiles were generated to analyze lncRNA expression with relation to different aspects of the disease (i.e., diagnosis, disease subtypes, cytogenetic and mutational aberrations, and risk of progression).

overall_design: Gene expression profiles of lncRNAs together with protein-coding genes were examined in  CD34+ bone marrow cells isolated from a cohort of 54 patients with myelodysplastic syndromes, 14 patients with acute myeloid leukemia with myelodysplasia-related changes, and 9 healthy donors.

first: Katarina

last: Szikszai

first: Zdenek

last: Krejcik

first: Jiri

last: Klema

first: Nikoleta

last: Loudova

first: Andrea

last: Mrhalkova

first: Monika

last: Belickova

first: Jitka

last: Vesela

last: Hruba

first: Viktor

last: Stranecky

first: David

last: Kundrat

first: Jaroslav

last: Cermak

first: Anna

last: Jonasova


title: Effect of dietary fats on liver transcriptome in pigs, estimated by 3`quant mRNA-seq

status: Public on Jan 25 2020

city: balice

first: Maria

last: Oczkowicz

state: malopolskie

address: krakowska 1

institute: National Reseach Institute of Animal Production

summary: We report the anaysis of the effect of the source of dietary fat (rapeseed oil, beef tallow, coconut oil) on the liver transcriptome. We observed significant changes in the expression of genes engaged incholesterol and bile acid biosynthesis, protein folding and processing, immunity, thyroid hormone metabolism and ER stress. .

overall_design: Examination of 3 different diets (n=5, n=5, n=6)  in one porcine tissue

first: Tomasz

last: Szmatoła


title: Microarray data for inflammatory breast cancer cases

status: Public on Jan 24 2020

city: Brasília

first: Rolando

middle: Andre Rios

last: Villacis

state: DF

address: Asa Norte

department: Genetics and Morphology

country: Brazil

institute: University of Brasília - UnB

summary: Inflammatory breast cancer (IBC) is a rare and aggressive type of breast cancer (BC) whose molecular basis is poorly understood. We performed a comprehensive molecular analysis of 24 fresh frozen IBC biopsies naïve of treatment, using a high-resolution microarray platform  The most common genes covered by copy number alterations included gains of MYC and MDM4, and losses affecting TP53 and RB1. MYC and MDM4 genes have been related to IBC aggressiveness, and MDM4 might also represent a new therapeutic target in IBC. Thirteen IBC cases presented copy-neutral of heterozygosity (cnLOH) or losses covering CHL1, which gives additional evidence of its role as a tumor suppressor. Functional enrichment analysis with the most common alterations revealed genes associated with inflammatory regulation and immune response. Particularly, IL6R and IL7 could represent therapeutic targets for IBC treatment. Chromothripsis patterns were identified in nine cases and chromosomal instability in 50% of cases. High homologous recombination (HR) deficiency scores were observed in triple-negative IBC and those with metastasis. High telomeric allelic imbalance (TAI) score was detected in patients having worse overall survival (OS). TAI score could also be useful to predict deficiency in homologous recombination (HR) genes and to identify patients for platinum or PARP inhibitor therapy. Our study describes the most common genomic alterations in IBC and their association with clinical findings, providing a framework for improved diagnosis and therapeutic opportunities for this aggressive tumor type.

overall_design:
Genomic DNA was isolated from fresh-frozen IBC tissue biopsies. The CytoScan HD Array (Affymetrix, Santa Clara, CA, USA) platform was used to evaluate CNAs and copy-neutral loss of heterozygosity (cnLOH) according to the manufacturer's recommendations.
The microarray analyses were performed using ChAS (Chromosome Analysis Suite), CoNVaQ and WebGestalt (WEB-based Gene SeT AnaLysis ToolKit) softwares. Additionally, microarray data was also used to estimate chromothripsis, genomic instability and homologous recombination deficiency scores.


title: Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay

status: Public on Feb 28 2020

city: Cambrdige

first: Jennifer

last: Hammelman

state: MA

address: 32 Vassar Street

institute: MIT

summary: Here we introduce the Multiplexed Integrated Accessibility Assay (MIAA), a multiplexed parallel reporter assay which measures changes to genome accessibility as a result of the integration of synthetic oligonucleotide phrase libraries into a controlled, natively inaccessible genomic context. We apply MIAA to measure the effects of sequence motifs on cell type-specific DNA accessibility between mouse embryonic stem cells and embryonic stem cell-derived definitive endoderm cells, screening a total of 7,905 distinct phrases. MIAA is able to recapitulate differential accessibility patterns of 100-nt sequences derived from natively differential genomic regions, identifying the presence of E-box motifs common to epithelial-mesenchymal transition driver transcription factors in stem cell-specific accessible regions that become repressed during differentiation to endoderm. We further present causal evidence that a single binding motif for a key regulatory transcription factor is sufficient to open chromatin, and classify sets of stem cell-specific, endoderm-specific, and shared pioneer factor motifs. We also demonstrate that over-expression of two definitive endoderm transcription factors, Brachyury and FoxA2, results in changes to accessibility in phrases containing their respective DNA-binding motifs. Finally, we use MIAA results to explore the order of motif interactions and identify preferential motif ordering arrangements that appear to have an effect on accessibility.

overall_design: SLOTv3 (de novo motif) Library - 2 replicates uCd8 locus in endoderm and stem cell; 4 replicates (stem cell) and 2 replicates (endoderm) in main explerimental RAR locus; 2 replicates FoxA2 and Brachyury over-expression SLOTv4 (pioneer) Library - 2 replicates of endoderm and stem cell

first: Richard

last: Sherwood


title: Nuclear control of mitochondrial function mediated by Zbtb11

status: Public on Jan 14 2020

city: London

first: Vlad

middle: Cezar

last: Seitan

address: Guy's Hospital

department: Medical & Molecular Genetics

institute: King's College London

summary: Zbtb11 is an uncharacterised transcription factor that is conserved in vertebrates. Mutations in its human gene cause a form of inherited intellectual disablity, while in zebrafish Zbtb11 mutations lead to impaired hematopoesis and neruonal development. We used a combination of functional genomics approaches to determine its functions.     To determine the genomic Zbtb11 binding locations, we carried out ChIP-seq using FLAG antibodies in a cell line with the endogenous Zbtb11 N-terminally tagged with FLAG (Zbtb11 FLAG/FLAG), as well as using an anti-Zbtb11 antibody in a wild type line.   To determine the genes regulated by Zbtb11 we generated an inducible KO line (Zbtb11 lox/lox, Rosa26 ERt2-Cre) that allows the rapid depletion of Zbtb11 upon treatment with 4-hydroxytamoxyfen (4OHT). We treated Zbtb11 lox/lox, Rosa26 ERt2-Cre cells either with 4OHT (Zbtb11 KO) or ethanol (EtOH) as control, and subsequently performed directional RNA-seq from samples collected 48 hours post-treatment. As control for the effect of 4OHT on gene expression, we also compared Zbtb11 KO cells to wild type cells treated with 4OHT.    The two ChIP-seq approaches showed very good overlap and allowed us to generate a set of high-confidence Zbtb11 binding sites common to both peak sets. We found Zbtb11 preferentially binds to a subset of house-keeping genes among which genes encoding proteins with mitochondrial functions are enriched. Upon Zbtb11 deletion, 154 genes changed expression 48 hours later, the vast majority of them down-regulated. Integration of ChIP-seq and RNA-seq data allowed us to identify the genes directly regulated by Zbtb11, and these were significantly enriched in genes with mitochondrial functions, with respiratory complex I and mitoribosome biogenesis being the overrepresented pathways. Subsequent biochemical experiments confirmed Zbtb11 is required for respiratory complex I assembly and for mitochondrial translation. In agreement with these findings Zbtb11 KO led to impaired respiration, proliferation arrest and cell death.

overall_design: ChIP-seq for Zbtb11 in mouse ES cells; and RNA-seq to determine differentially expressed genes upon induction of Zbtb11 KO

first: Brooke

last: Wilson

first: Ambra

last: Annibali

first: Lena

last: Boehme

first: Alan

last: Hodgkinson

first: Thomas

last: Carroll

first: Rebecca

middle: J

last: Oakey


title: Integrative genomic and epigenomic profiling reveals cell-type specific signaling networks in activated lung mononuclear phagocytes [RNA-seq]

status: Public on Jan 20 2020

city: La Jolla

first: Eniko

last: Sajti

state: CA

address: 9500 Gilman Drive

department: Pediatrics

institute: UCSD

summary: The lung is inhabited by resident alveolar and interstitial macrophages as well as monocytic cells that survey the lung. Each cell type plays distinct functional roles under homeostatic and inflammatory conditions, but mechanisms establishing their molecular identities and functional potential remain poorly understood. Here, systematic evaluation of transcriptomes and open chromatin of alveolar macrophages (AMs), interstitial macrophages (IMs) and lung monocytes from two mouse strains enabled inference of common and cell-specific transcriptional regulators.  We provide evidence that these factors drive selection of regulatory landscapes that specify distinct phenotypes of AMs and IMs and entrain qualitatively different responses to TLR4 signaling in vivo.  These studies reveal a striking divergence in a fundamental innate immune response pathway in AMs and establish a framework for further understanding macrophage diversity in the lung.

overall_design: Low input RNA-seq for alveolar macrophages (AM), interstitial macrophages (IM) and inflammatory monocytes (iMo) isolated from the lung of C57BL/6J mice after intraperitoneal LPS and intranasal LPS administration respectively at 0h, 2h, 6h and 22h.

first: Verena

last: Link

first: Zhengyu

last: Ouyang

first: Nathanael

last: Spann

first: Emma

last: Westin

first: Casey

last: Romanoski

first: Gregory

last: Fonseca

first: Lawrence

last: Prince

first: Christopher

middle: K

last: Glass


title: Transcriptional changes in Krt13 knockout mouse tongues

status: Public on Feb 13 2020

city: Madison

first: Hao

last: Chang

state: WI

address: 1300 University Ave

department: Dermatology

institute: University of Wisconsin-Madison

summary: We used RNA-Seq to search for potential downstream effectors of Krt13 during the development of White Sponge Nevus-like phenotype in mice

overall_design: We profiled the transcriptomes of whole P0 tongues and P20 ventral tongues from wild type and Krt13 knockout mice. Four or five biologically independent samples were collected for each genotype.


title: Alteration of genome folding via engineered transposon insertion [HiC]

city: University Park

first: Ross

last: Hardison

address: 303 Wartik Lab

institute: Pennsylvania State University

summary: Mammalian chromosomes are partitioned into contact domains that can be conserved as functional units in evolution. Disruptions of domains can result from perturbed CTCF, cohesin, or chromosomal rearrangements. However, to what extent domains can be created de novo has not been explored in depth. Here, using a gain-of-function approach leveraging genome editing and Hi-C, we examined whether, and how, a putative boundary element can function to organize de novo domains in the context of multiple ectopic insertion sites. We subsequently dissected the distinct roles of the CTCF binding site and the transcription start site within the insertion element in changing genome folding.

overall_design: Using a transposon-based approach, we inserted a 2 kb DNA fragment, which resides within a tissue-invariant domain boundary, into the genomes of near-haploid HAP1 cells. Following transposition, we established clonal lines and prioritized Clones 21 (C21) and 25 (C25), which contained ten and six insertions, respectively, across a total of 11 chromosomes. We then performed in situ Hi-C on edited clones and unedited parental (WT) cells to characterize how the insertion of a boundary-associated DNA fragment shapes human genome architecture. Furthermore, we carried out a series of CRISPR-based editing experiments to dissect how the TSS and the CTCF binding site within the insertion element contributes to new domain formation. Additionally, we used CRISPR to delete the endogenous 2 kb element and characterized its function at its endogenous boundary. In addition to Hi-C, we performed Capture-C, ChIP-seq (CTCF, Rad21, and H3K27Ac), and RNA-seq to further characterize the structural changes resulting from each round of genome editing experiments.

first: Di

last: Zhang

first: Peng

last: Huang

first: Sharma

last: Malini

first: Cheryl

last: Keller

first: Belinda

last: Giardine

first: Haoyue

last: Gilgenast

first: Jennifer

last: Phillips-Cremins

first: Gerd

last: Blobel


title: Integrative genomic and epigenomic profiling reveals cell-type specific signaling networks in activated lung mononuclear phagocytes

first: Eniko

last: Sajti


title: p53 activates the long noncoding RNA Pvt1b to inhibit Myc and suppress tumorigenesis

city: New Haven

first: Nadya

last: Dimitrova

state: CT

address: 260 Whitney Ave YSB211

department: MCDB

institute: Yale University


title: Prediction of prognostic signatures in triple-negative breast cancer based on the differential expression analysis via NanoString nCounter immune panel

status: Public on Jan 08 2020

city: Seoul

first: Gyeong Back

last: Lim

address: 79, Sangdo-ro 37-gil, Dongjak-gu, Seoul, Republic of Korea

institute: Asan Medical Center

summary: Triple Negative Breast Cancer (TNBC) has been considered an aggressive and complex subtype of breast cancer. Current biomarkers used in breast cancer treatment are highly dependent on targeting ER, PR, or HER2 in clinical practice, which results in ttreatment failure and disease recurrence continue to be clinically challenging. In this regards, there is still a crucial need for improvement of TNBC treatment by discovery of effective biomarkers that can be easily translated to the clinics and possible targets as prognosis and novel therapies.   This study reports an approach for biomarker discovery, which predicts tumour relapse and pathologic complete response (pCR) in TNBC on the basis of mRNA expression quantified using NanoString nCounter Immunology Panel. We identify nine and 13 differentially expressed genes (DEGs), respectively, that are strongly associated with pCR and relapse from  579 immune genes  over a small number of samples  (n=55) using edgeR. To overcome a small sample size limitation, prediction models based on the random forest are constructed on the DEGs as selected features extracted from the DEG analysis. Comprehensive analysis indicated that our prediction models outperform those constructed on features extracted from the existing feature selection model such as, Elastic Net in terms of accuracy. The prediction models are assessed by randomization test to validate the robustness (empirical P for the model of pCR= 0.022 and empirical P for the model of relapse= 0.025). Furthermore, three DEGs (IL17B, EDNRB, and TGFBI) in the model of relapse show prognostic significance to predict cancer patient survival through Cox proportional hazards regression model based survival analysis.

overall_design: Paraffin-embedded tissue biopsy samples from 55 Among 108 TNBC patients diagnosed and treated with anthracycline and taxane-based NAC and by surgery from 2010 to 2012 at Asan Medical Centre, paraffin-embedded tissue samples  from 55 patients were processed using GX Human Immunology V2kit for NanoString nCounter Gene expression for a total of 579 immunology-related human genes. Among 55 cases, operation specimens from 14 patients, including 6 cases of pCR, were also analysed. Tthe patient's clinical data including survival time, survival parameters, and chemotherapeutic responsiveness (pCR, residual cancer burden, RCB, Miller Payne grade), relapse and pCR under PRE and POST conditions, were collected

first: Young-Ae

last: Kim

first: Gyeong

first: Jeong-Han

last: Seo

first: Sung

last: Park

first: Hee

last: Lee

first: Gyungyub

last: Gong


title: Comparative transcriptomics and co-expression networks reveal tissue- and genotype-specific responses to reproductive-stage drought stress in rice (Oryza sativa L.) [panicle]

first: Jeshurun Asher

last: Tarun

summary: Purpose: The goal of the study is to compare the transcriptomic differences of the panicle tissue at the reproductive-stage of the Introgression Line (IR 96321-1447-165-B-3-1-2), which is drought-tolerant, to Swarna (recipient parent), which is drought-sensitive.

overall_design: Panicle mRNA profiles 2x2 factorial experiment under control and drought stress condition at the reproductive-stage of IL (drought-tolerant) and Swarna (drought-sensitive) were generated by deep sequencing with four independent biological replicates of each genotype under each conditions using Illumina HiSeq 2000.

first: Jeshurun

first: Tobias

last: Kretzschmar


title: The Xenobiotic Transporter Mdr1 Enforces T Cell Homeostasis in the Presence of Intestinal Bile Acids [shMdr1 RNA-seq in vivo]

status: Public on Jan 10 2020

city: Jupiter

first: Mark

last: Sundrud

state: FL

address: 120 Scripps Way

department: Immunology and Microbiology

institute: The Scripps Research Institute

summary: CD4+ T cells are tightly regulated by microbiota in the intestine, but whether intestinal T cells interface with host-derived metabolites is less clear. Here, we show that CD4+ T effector (Teff) cells upregulated the xenobiotic transporter, Mdr1, in the ileum to maintain homeostasis in the presence of bile acids. Whereas wild-type Teff cells upregulated Mdr1 in the ileum, those lacking Mdr1 displayed mucosal dysfunction and induced Crohn’s disease-like ileitis following transfer into Rag1-/- hosts. Mdr1 mitigated oxidative stress and enforced homeostasis in Teff cells exposed to conjugated bile acids (CBAs), a class of liver-derived emulsifying agents that actively circulate through the ileal mucosa. Blocking ileal CBA reabsorption in transferred Rag1-/- mice restored Mdr1-deficient Teff cell homeostasis and attenuated ileitis. Further, a subset of ileal Crohn’s disease patients displayed MDR1 loss of function. Together, these results suggest that coordinated interaction between mucosal Teff cells and CBAs in the ileum regulate intestinal immune homeostasis.

overall_design:
RNA-seq of approximately 10,000 sorted congenic CD4+ Teff cells tranduced with shCD8 or shMdr1 isolated from small intestine lamina propria  or spleen from Rag deficient hosts that have or lack Asbt at 6 weeks post T cell transfer
8 samples, 1 replicate each

first: M

last: Chen


title: Targeted epigenetic modulation using a DNA-based histone deacetylase inhibitor enhances cardiomyogenesis in mouse embryonic stem cells (Chem-Seq)

status: Public on Jan 03 2020

city: Suwon

first: Jin-A

address: 2066 Seoburo

department: School of medicine

institute: Sungkyunkwan university

summary: We used Chem-seq to map the genome-wide distribution of the binding sequence of SAHA-PIP G.

overall_design: Examination of Biotin-SAHA-PIP-G sample

first: Kyeong


title: Targeted epigenetic modulation using a DNA-based histone deacetylase inhibitor enhances cardiomyogenesis in mouse embryonic stem cells (ChIP-Seq)

summary: To determine how SAHA-PIP G can trigger the expression of the mesendoderm-related genes in mouse ES cells, chromatin immunoprecipitation (ChIP-seq) analysis was carried out with an antibody against the histone H3 lysine 4 trimethylation (H3K4me3) using EBs harvested on day 0

overall_design: Examination of H3K4me3 in 2 embryonic body types that with/without 1 μM SAHA-PIP G treatment.


title: Integrative genomic and epigenomic profiling reveals cell-type specific signaling networks in activated lung mononuclear phagocytes [RNA-seq/ATAC-seq]

overall_design: RNA-seq and ATAC-seq experiments (in replicates) for two different strains of mic (C57BL6/J and DBA/2J) in alveolar macropaghes (AM), interstital macrophages (IM), inflammatory monocytes (iMo) and patrolling monocytes (pMo)

first: Christopher

last: Glass


title: Targeted epigenetic modulation using a DNA-based histone deacetylase inhibitor enhances cardiomyogenesis in mouse embryonic stem cells

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

overall_design: Refer to individual Series


title: Probiotic Bacillus subtilis CW14 Reduces the Epithelial Barrier Disruption and Toxicity of Ochratoxin A to Caco-2 cells

status: Public on Dec 31 2019

city: Beijing

first: Peng

last: Meng Xue

address: 17 Qinghua Donglu

institute: China Agricultural university

summary: The multiple toxic effects of Ochratoxin A(OTA) are a real threat for human beings and animal health. It has been suggested that probiotic improve the epithelial barrier disruption and reduce cell damage induced by mycotoxins. However, the exact effect and mechanism of probiotic Bacillus subtilis CW14 on epithelial barrier function is not well understood. The aim of this study was to examine whether B. subtilis CW14 could protect against OTA-induced barrier disruption and cell damage in human intestinal epithelial cell line (Caco-2). The results showed that OTA was absorbed efficiently in Caco-2 cells, led to microvilli disruption and tight junction protein(ZO-1 and claudin-1) damage, and suppressed cell proliferation by arresting cell cycle in G2/M phase and promoting apoptosis. The addictive of B. subtilis CW14 strains could partially reversed the tight junction injury by improving the ZO-1 protein expression and reduced the apoptosis induced by OTA. Furthermore, the transcriptome analysis data indicated that OTA mainly down-regulated the gene expression involved in tight junctions, cell cycle, and apoptosis-related signaling pathways. While the B. subtilis CW14 has the potential to protect epithelial barrier through activating the toll-like receptor signaling pathway, and could partially repair the OTA damage by down-regulating the TRAIL death receptor genes and up-regulating the DNA repair genes. Our findings suggest an important implication for the role of B. subtilis CW14 on the regulation of tight junction proteins and reduction cell death in intestine epithelial cells, and that is a potential candidate as a food additive to protect against intestinal damage.

overall_design: Four groups, three replicates (12 arrays in total):1. Control group×3; 2. B. subtilis CW14 treatment group×3; 3. OTA treatment group×3; 4. OTA and B. subtilis CW14 co-treatment group×3.

first: Mengxue

last: Peng

first: Jiawei

last: Liu

first: Zhihong

last: Liang


title: An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease (H3K9ac, H3K27ac, H3K122ac, H3K4me1) [ChIP-Seq]

status: Public on Jan 01 2020

city: Philadelphia

first: Yemin

last: Lan

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: We report the epigenetic landscape of multiple histone marks in human hippocampus subject to normal aging and Alzheimer's disease.

overall_design: H3K27ac, H3K9ac, H3K122ac and H3K4me1 ChIP-seq in postmortal lateral temporal lobe of Alzheimer's disease affected brains (AD), control Old (Old) and control Young (Young).

first: Raffaella

last: Nativio

first: Berger

last: Shelley


title: Bone marrow-derived non-transformed murine macrophages with an unlimited self-renewing ability

status: Public on Dec 27 2019

city: Kumamoto

first: Hesham

middle: Elsayed

last: Nasser

state: Kumamoto

address: 2-2-1 Honjo, Chou-ku

department: Infection and Hematopoiesis

country: Japan

institute: Joint Research Center for Human Retrovirus Infection, Kumamoto University

summary:
Tissue macrophages derive from bone marrow monocytes, and recent studies using mice have revealed that they also derive from yolk sac precursors or fetal liver monocytes. However, embryo-derived macrophages are supposed to be more important to maintain tissue macrophage pool because they can self-renew. Here, we show that adult bone marrow-derived macrophages (MDM) also retain the ability of self-renewal. Where they were readily obtained by a long-term culture: mouse bone marrow cells were cultured with macrophage colony-stimulating factor (M-CSF). After several passages, most MDM died owing to their limited life span with survival and expansion of self-renewing macrophages resided in a small fraction. Self-renewing macrophages were not tumorigenic, but proliferate for a long period in almost unlimited numbers. Despite being distinct from MDM, they were phenotypically and functionally differentiated macrophages, and could differentiate into dendritic cells or osteoclasts. Moreover, Krüppel-like Factor 2 (KLF2) involved in self-renewal of embryonic stem cells, was markedly up-regulated by M-CSF-stimulation in self-renewing macrophages, which was accompanied with a gradual down-regulation of MafB, a suppressor of KLF2 expression. Importantly, knockdown of KLF2 as well as c-Myc caused cell cycle arrest, apoptosis, and diminished cell growth. Our culture method results suggest the presence of precursor(s) for self-renewing macrophages in adult bone marrow that can be used to describe discrepancy of adult- and embryo-derived macrophages.
Microarray data from both monocyte-derived and bone marrow-derived mouse macrophages are used to detail the global gene expression profile underlying phenotype, function and self-renewal capacity in order to unravel difference/similarity in phenotype/function and mechanism/degree of self-renewal between the two distinct macrophages.

overall_design: In order to identify drivers of self-renewal capacity in macrophages (e.g. transcription factors), microarray data of mouse bone marrow monocyte -derived (primary) macrophages at Day 5 (AR2522_01) and bone marrow-derived self-renewing macrophages after four passages (AR2522_02) were analyzed.

first: Partho

last: Adhikary

first: Amira

last: Abdel-Daim

first: Osamu

last: Noyori

first: Ryusho

last: Kariya

first: Seiji

last: Okada

first: Wenjuan

last: Ma

first: Masaya

last: Baba

first: Hitoshi

last: Takizawa

first: Mariko

last: Yamane

last: Niwa

first: Shinya

last: Suzu


title: Gene expression in non-involved areas of villin-TLR4 and wild-type littermate mice undergoing a colitis-associated cancer model

city: Miami

first: Juan

middle: F

last: Burgueno

address: 1011 NW 15th St, Gautier Bldg. suite 534B

institute: University of Miami

summary: Villin-TLR4 mice and their wild-type littermates underwent the AOM-DSS model of tumorigenesis and their non-involved tissues were analyzed for transcriptomic expression

overall_design: Mice were treated with 7.4 mg/kg AOM and 2 cycles of DSS. At day 56, mice were euthanized and tissues from areas that did not develop tumors were analyzed

first: Julie

last: Davies

first: Rebeca

last: Santaolalla

first: Maria

last: Abreu


title: Expansion of the circadian transcriptome in Brassica rapa supports genome wide diversification of homeolog gene expression patterns

status: Public on Jan 31 2020

city: Hanover

first: Kathleen

last: Greenham

state: NH

address: 78 College St.

department: Biological Sciences

institute: Dartmouth College

summary: Following divergence from Arabidopsis thaliana, Brassica rapa underwent a whole genome triplication followed by extensive genome fractionation. Preferential retention of circadian clock genes suggest that expansion of the circadian network may play an important role during B. rapa domestication. To characterize the circadian transcriptome network, RNA-seq was performed in the B. rapa oil-type variety R500 following photocycle and thermocycle circadian time courses. The photocycle (LDHH) time course consisted of growing plants for 15 days at 20°C under a 12h light/12h dark photoperiod and transfering plants to constant light and 20°C 24h prior to harvesting leaf tissue every 2h for 48h starting at ZT24 with 2 biological replicates at every time point. The thermocycle (LLHC) time course consisted of growing plants for 15 days under constant light with a 12h 20°C/12h 10°C thermoperiod and transfering plants to constant light and 20°C 24h prior to harvesting leaf tissue every 2h for 48h starting at ZT24 with 2 biological replicates at every time point.

overall_design: Brassica rapa subsp. trilocularis (R500) plants were grown under photocycle (LDHH) 12h light at 20°C/12h dark at 10°C and thermocycle (LLHC) 12h light at 20°C/12h light at 10°C conditions for 15 days after sowing (DAS) before transfering to constant light and 20°C (LLHH). Starting 24h after transfer to LLHH, leaf tissue was collected every 2h for 48h. We collected 2 replicates for every time point.

first: Ryan

last: Sartor

first: Ping

last: Lou

first: Todd

last: Mockler

first: C

middle: R

last: McClung


title: Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas

status: Public on Jan 13 2020

city: New York

first: Itai

last: Yanai

state: NY

address: 435 E. 30th Street, 8th Floor

institute: Institute for Computational Medicine, NYU Langone Health

summary: Single-cell RNA sequencing (scRNA-seq) enables the systematic identification of cell populations in a tissue, but characterizing their spatial organization remains challenging. We combine a microarray-based spatial transcriptomics method that reveals spatial patterns of gene expression using an array of spots, each capturing the transcriptomes of multiple adjacent cells, with scRNA-Seq generated from the same sample. To annotate the precise cellular composition of distinct tissue regions, we introduce a method for multimodal intersection analysis. Applying multimodal intersection analysis to primary pancreatic tumors, we find that subpopulations of ductal cells, macrophages, dendritic cells and cancer cells have spatially restricted enrichments, as well as distinct coenrichments with other cell types. Furthermore, we identify colocalization of inflammatory fibroblasts and cancer cells expressing a stress-response gene module. Our approach for mapping the architecture of scRNA-seq-defined subpopulations can be applied to reveal the interactions inherent to complex tissues.

overall_design: Single-cell RNA-sequencing and spatial transcriptomics of primary pancreatic cancer tissue from six patients.

first: Reuben

last: Moncada


title: Uncovering the hepatic gene expression variations and sex-differences as response to high-fat diet consumption in the highly genetically diversity of the Collaborative Cross mouse model

status: Public on Dec 10 2019

city: Athens

first: Aristotelis

last: Chatziioannou

address: 48 Vassileos Constantinou Avenue

country: Greece

institute: National Hellenic Research Foundation

summary: Hepatic gene expression variations and sex-differences due to high-fat diet consumption using the Collaborative Cross mouse model

overall_design: 84 samples, Diabetic, Obese, or Healthy for each condition

first: Georgia

last: Kontogianni

first: Hanifa

last: Abu-Toamih Atamni

first: Ilona

last: Binenbaum

first: Fuad

last: Iraqi


title: Large-scale screening of circulating microRNAs in individuals with HIV-1 mono-infections reveals specific liver damage signatures

status: Public on Dec 06 2019

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

institute: IGTP

summary: Human immunodeficiency virus type 1 (HIV-1)-induced inflammation and/or long-term antiretroviral drug toxicity may contribute to the evolution of liver disease. We investigated circulating plasma microRNAs (miRNAs) as potential biomarkers of liver injury in patients mono-infected with HIV-1. We performed large-scale deep sequencing analyses of small RNA level on plasma samples from patients with HIV-1 mono-infection that had elevated or normal levels of alanine aminotransferase (ALT) or focal nodular hyperplasia (FNH). Hepatitis C virus (HCV) mono-infected patients were also studied. Compared to healthy donors, patients with HIV-1 or HCV mono-infections showed significantly altered (fold change >2, adjusted p<0.05) level of 25 and 70 miRNAs, respectively. Of the 25 altered miRNAs found in patients with HIV-1, 19 were also found in patients mono-infected with HCV. Moreover, 13 of the 14 most up-regulated miRNAs (range: 9.3-3.4-fold increase) in patients with HCV mono-infections were also up-regulated in patients with HIV-1 mono-infections. Importantly, most of these miRNAs significantly and positively correlated with ALT and aspartate aminotransferase (AST) levels, and liver fibrosis stage (p<0.05). MiR-122-3p and miR-193b-5p were highly up-regulated HIV-1 mono-infected patients with elevated ALT or FNH, but not in HIV-1 patients with normal levels of ALT. These results reveal that HIV-1 infections impacted liver-related miRNA levels in the absence of an HCV co-infection, which highlights the potential of miRNAs as biomarkers for the progression of liver injury in HIV-1 infected patients.

overall_design: In total 97 plasma derived small RNA samples were analyzed: 21 from healthy reference and 76 from virally mono-infected individuals. There were two patient groups based on virus infection status: a group of 22 individuals infected with hepatitis C virus (HCV), and a group of 54 individuals infected with human immunodefficency virus (HIV). The study focused on determining miRNA expression differences in the context of liver damage. Among  HIV mono-infected there were 22 with normal ALT levels, 21 with ALT levels above the upper limit of normal and 11 with biopsy proven nodular regenerative hyperplasia (NH). All samples were controlled for hemolysis using a qPCR based test taking only samples with miR-451/miR-23a ratios with ΔCt<7 (range −0.04 to 6.3; average 3.53). Design efforts were made to randomize all subgroups to be equally represented in the library preparation and size selection steps to be able to correct for possible batch effects. The experiment was performed in the context of a larger sample set including a total of 144 samples. Size selection was performed in pools of 24 libraries, and 3 sets of 2 library pools were merged into 3 superpools of 48 samples each for Illumina sequencing. In the final analysis 6 samples were excluded from the final differential miRNA expression analysis as they showed outlier behavior in unsupervised exploratory pricipal components analysis: 5 HCV monoinfected and 1 HIV infected with elevated ALT. Thus, final results of this work were derived from 91 samples comparing: 21 healthy, 17 HCV monoinfected, 22 HIV mono-infected with normal ALT, 20 HIV mono-infected with elevated ALT, and 11 HIV mono-infected with NH.

first: Sandra

last: Franco

first: Daniela

last: Buccione

first: Raquel

last: Pluvinet

first: Beatriz

last: Mothe

first: Lidia

last: Ruiz

last: Nevot

first: Ana

last: Jordan-Paiz

first: Laia

last: Ramos

first: Susanna

last: Aussó

first: Rosa

last: Morillas

first: Miguel

last: Martinez

first: Cristina

last: Tural


title: High-throughput transcriptome analysis of clinical psoriasis

status: Public on Dec 25 2019

city: Shanghai

first: Zengyang

last: Yu

address: 301 Yanchang Road

institute: Shanghai Tenth People's Hospital, Tongji University School of Medicine

summary:
Purpose: The present study is aiming to understand transcriptome changes during psoriatic changes using high-throughput sequencing and thereby comprehensively assess the diseases and guide future research directions.
Methods: Clinical psoriatic samples, including psoriatic lesions and their adjacent normal skin samples, and the surgical derived skins from healthy individuals as comparative controls were collected and analysed of their RNA expression profile using Illumina HiSeq 4000. raw sequencing reads were processed and pre-qualified using Trimmomatic and Fragments Per kb Per Million Reads (FPKM) method was used to calculate the abundance of each transcript followed by Negative Binomial Distribution tests to identify significant differences in each comparison.
Results: Total reads for mRNAs, lncRNAs and miRNAs was 108,552, 105,136 and 2762, respectively, including 649 novel lncRNAs and 905 novel miRNAs. 5383 DE_mRNAs, 1201 DE_lncRNAs and 80 DE_miRNAs were identified in the comparison of the psoriasis lesions-adjacent normal group (PN) vs. healthy control-derived normal skin group (NN; PN vs. NN). A total of 9513 DE_mRNAs, 1940 DE_lncRNAs and 251 DE_miRNAs were identified in the psoriasis lesion group (PS) vs. NN comparison (PS vs. NN), and 4946 DE_mRNAs, 1559 DE_lncRNAs and 92 DE_miRNAs were identified in the PS vs. PN comparison.
Conclusions: We identified numerous differentially expressed RNAs, including mRNAs, long non-coding RNAs (lncRNAs) and microRNAs (miRNAs). Our results reveal transcriptomic changes, expand our mechanistic understanding of psoriasis, and may lead to new directions for psoriasis research.

overall_design: Five adult  psoriasis patients were recruited in this study, none of which had received systematic treatment and all were free from medical treatment within the 3 months before recruitment. Psoriatic plaque tissue (PS) and adjacent normal skin tissue (PN) was taken from each patient, and five control skin samples were obtained from surgical discard specimens of healthy people (NN). Total RNA was isolated and sequencing was conducted with a HiSeq 4000 (Illumina).

first: Yuling

last: Shi


title: Integrative genomic and epigenomic profiling reveals cell-type specific signaling networks in activated lung mononuclear phagocytes [scRNA-seq]

first: Eniko

last: Sajti

summary: The lung is inhabited by resident alveolar and interstitial macrophages as well as monocytic cells that survey the lung. Each cell type plays distinct functional roles under homeostatic and inflammatory conditions, but mechanisms establishing their molecular identities and functional potential remain poorly understood. Here, systematic evaluation of transcriptomes and open chromatin of alveolar macrophages (AMs), interstitial macrophages (IMs) and lung monocytes from two mouse strains enabled inference of common and cell-specific transcriptional regulators.  We provide evidence that these factors drive selection of regulatory landscapes that specify distinct phenotypes of AMs and IMs and entrain qualitatively different responses to TLR4 signaling in vivo.  These studies reveal a striking divergence in a fundamental innate immune response pathway in AMs and establish a framework for further understanding macrophage diversity in the lung.

overall_design: Single-cell RNA-seq of FACS we isolated lung myeloid cells from 2 week old male DBA/2J mouse.

first: Verena

last: Link

first: Zhengyu

last: Ouyang

first: Nathanael

last: Spann

first: Emma

last: Westin

first: Casey

middle: E

last: Romanoski

first: Gregory

last: Fonseca

first: Lawrence

last: Prince

first: Christopher

last: Glass


title: Domoic acid disruption of neurodevelopment and behavior involves altered myelination in the spinal cord

city: Woods Hole

first: Jennifer

middle: Martinez

last: Panlilio

address: 266 Woods Hole Road

department: Biology

institute: Woods Hole Oceanographic Institution

summary: Harmful algal blooms (HABs) produce potent neurotoxins that threaten human health. Early life exposure to low levels of the HAB toxin domoic acid (DomA) can produce long-lasting behavioral deficits, but the mechanisms involved are unknown. Using the zebrafish model, we investigated the developmental window of susceptibility to low doses of DomA and examined cellular and molecular targets. Larvae exposed to DomA (0.09 ng) at 2 days post-fertilization (dpf), but not at 1 or 4 dpf, showed deficits in startle behavior that included reduced responsiveness and altered kinematics. Similarly, myelination in the spinal cord was disorganized after exposure at 2 dpf but not 1 or 4 dpf. Time-lapse imaging revealed disruption of the initial stages of myelination. DomA down-regulated genes required for maintaining myelin structure and the axonal cytoskeleton. These results identify a developmental window of susceptibility to DomA-induced behavioral deficits involving altered gene expression and disrupted myelin structure and establish a zebrafish model for investigating the underlying mechanisms.

overall_design: 12 samples were sequenced, including 2 different treatments across 2 different developmental periods. Each treatment has 3 biological replicates

first: Neelakanteswar

last: Aluru

first: Mark

last: Hahn


title: Early chromatin shaping predetermines multipotent vagal neural crest into neural, neuronal and mesenchymal lineages [CRISPR RNA-seq]

status: Public on Nov 27 2019

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

institute: MRC Weatherall Institute of Molecular Medicine

summary: The enteric nervous system (ENS) predominantly originates from vagal neural crest cells (VNC) that emerge from the caudal hindbrain, invade the foregut and populate the gastrointestinal tract. However, the gene regulatory network (GRN) orchestrating the early specification of VNC remains unknown. Using an EdnrB enhancer, we generated a comprehensive temporal map of the chromatin and transcriptional landscape of VNC in the avian model, revealing three VNC cell clusters (neural, neurogenic and mesenchymal), each predetermined epigenetically prior to neural tube delamination. We identify and functionally validate regulatory cores (Sox10/Tfap2B/SoxB/Hbox) mediating each programme and elucidate their combinatorial activities with other spatiotemporally-specific transcription factors (bHLH/NR). Our global deconstruction of the VNC-GRN in vivo sheds light on critical early regulatory mechanisms that may influence the divergent neural phenotypes in enteric neuropathies.

overall_design: Bulk RNA-seq was performed on neural crest cells dissected from the developing chick embryo to determine the effect of CRISPR/Cas9 knock down and its downstream effects on a set of putative core transcription factors.

first: Irving

last: Ling


title: Early shaping of the chromatin landscape specifies vagal neural crest into distinct lineages [RNA-seq]

summary: Complex traits in enteropathies like Hirschsprung disease underscores a larger gene regulatory network (GRN) driving vagal neural crest (VNC) to form the enteric nervous system (ENS). To dissect the GRN and understand the function of non-coding regulatory regions, we used a novel highly conserved EdnrB E2 enhancer with a FoxD3 NC2 enhancer to generate a comprehensive map of VNC chromatin and transcriptional landscape during ENS development. Together with single-cell transcriptional profiles, we revealed three distinct lineages of VNC (glial, neuronal, and mesenchymal) that are each pre-specified by independent GRNs before delamination. We identified and functionally validated regulatory cores mediating the glial (Tfap2B and Sox10) and neuronal programmes (Sox3/Msx1) that in spatiotemporal combinations with other families of transcription factors, control the timing of enteric cell differentiation. Deconstructing the VNC-GRN identifies factors that pre-specifies cells to their presumptive fate and sheds light on how early GRN dysregulations influence the divergent neural phenotype in enteropathies.

overall_design: Transcriptomic profilling of avian neural crest cells isolated from their in vivo context at HH12, HH18 and HH25