title: Translation control of the immune checkpoint in cancer and its therapeutic targeting

first: Zhen

last: Shi

address: 279 Campus Drive

institute: Stanford

summary: Cancer cells develop mechanisms to escape immunosurveillance, among which modulating the expression of immune suppressive messenger RNAs is most well-documented. However, how this is molecularly achieved remains largely unresolved. Here, we develop an in vivo mouse model of liver cancer to study oncogene cooperation in immunosurveillance. We show that MYC overexpression (MYCTg) synergizes with KRASG12D to induce an aggressive liver tumor leading to metastasis formation and reduced mouse survival compared with KRASG12D alone. Genome-wide ribosomal footprinting of MYCTg;KRASG12 tumors compared with KRASG12D revealed potential alterations in translation of mRNAs, including programmed-death-ligand 1 (PD-L1). Further analysis revealed that PD-L1 translation is repressed in KRASG12D tumors by functional, non-canonical upstream open reading frames in its 5′ untranslated region, which is bypassed in MYCTg;KRASG12D tumors to evade immune attack. We show that this mechanism of PD-L1 translational upregulation was effectively targeted by a potent, clinical compound that inhibits eIF4E phosphorylation, eFT508, which reverses the aggressive and metastatic characteristics of MYCTg;KRASG12D tumors. Together, these studies reveal how immune-checkpoint proteins are manipulated by distinct oncogenes at the level of mRNA translation, which can be exploited for new immunotherapies.

overall_design: To identify the transcripts specifically translated in primary liver tumors in MYC; KRAS(G12D) and KRAS(G12D) mice, we first carefully micro-dissected primary liver tumor nodules in MYC; KRAS(G12D) and KRAS(G12D) mice as well as wildtype (WT) controls. We sequenced total mRNAs (2 replicates each) and ribosome-protected mRNA fragments (RPFs) using ribosome profiling (2 replicates each) to generate genome-wide transcriptional and translational landscapes, respectively.

first: Yichen

last: Xu

first: Mauro

last: Poggio

first: Hyun

middle: Y

last: Jin

first: Craig

last: Forester

last: Wang

last: Stumpf

first: Lingru

last: Xue

first: Emily

last: Devericks

first: Lomon

last: So

first: Hao

last: Nguyen

first: Alice

last: Griselin

first: John

last: Gordan

first: Sarah

last: Umetsu

first: Siegfried

last: Reich

last: Worland

first: Saurabh

last: Asthana

first: Maria

last: Barna

first: Kevin

last: Webster

first: Tom

last: Cunningham

first: Davide

last: Ruggero


title: Inhibition of SF3B1 by molecules targeting the spliceosome in Rh18 cells

status: Public on Jan 14 2019

city: Memphis

first: Timothy

middle: Isham

last: Shaw

state: TN

address: 262 Danny Thomas Pl

department: Computational Biology

country: USA

institute: St Jude Children's Research Hospital

type: Expression profiling by high throughput sequencing

summary: In order to examine the effects of sudemycin D1 on the whole transcriptome, we exposed Rh18 cells to 1μM of drug for 8hr and after extraction, subjected RNA to RNAseq analysis. Control samples were treated with the vehicle (DMSO) alone and all analyses were conducted in triplicate.

overall_design: Compare differentially expressed genes in sudemycin treated verses control group.

first: Gang

last: Wu

first: Phillip

middle: M

last: Potter


title: DNA hypermethylation encroachment at CpG island borders in cancer is predisposed by H3K4 monomethylation [TAB-Seq]

status: Public on Jan 23 2019

city: Sydney

first: Ksenia

last: Skvortsova

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute

type: Methylation profiling by high throughput sequencing

summary: DNA methylation plays a key role in demarcation of regulatory regions, including promoter-associated CpG islands. While CpG islands are typically maintained in an unmethylated state in normal cells, a proportion of CpG islands are subject to hypermethylation in cancer cells. It still remains elusive how the exquisite demarcation of the bimodal methylation state is established and maintained at the CpG island flanks and conversely what triggers the erosion of CpG island DNA methylation in tumorigenesis. Here, we applied whole-genome bisulphite sequencing to study the comprehensive methylation patterns of prostate normal and cancer tissues. Alongside we performed TET-assisted bisulphite sequencing to study genome-wide DNA hydroxymethylation patterns of normal prostate and prostate cancer tissues.

overall_design: To investigate DNA hydroxymethylation patterns at CpG islands in normal prostate and prostate cancer, TET-assisted bisulphite treatment of 3 pairs of clinical benign-tumor samples was performed using the 5hmC TAB-seq Kit (WiseGene, USA, cat no K001).

first: Phuc-Loi

last: Luu

first: Elena

last: Zotenko

first: Susan

middle: J

last: Clark

first: Clare

last: Stirzaker


title: Whole transcriptome analysis reveals a pro-inflammatory profile of ductular reaction cells in AH.

status: Public on Jan 11 2019

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: Objective: Alcoholic hepatitis (AH) is characterized by the expansion of ductular reaction (DR) cells and expression of liver progenitor cell (LPC) markers. The aim of this study was to identify the gene expression profile and associated genes of DR cells and to evaluate its weight in alcoholic disease progression.  Design: KRT7+, KRT7- and total liver fractions were laser microdissected from liver biopsies (n=6) of patients with AH and whole transcriptome was sequenced. Gene signature was assessed in transcriptomic data from 41 patients with alcoholic liver disease. Pro-inflammatory profile was evaluated in tissue and serum samples and in human LPC organoids.  Results: Transcriptome analysis of KRT7+ DR cells uncovered intrinsic gene pathways of DR and allowed identifying genes associated with DR expressed in AH. In addition, DR gene signature and associated genes correlated with disease progression and poor outcome in AH patients. Importantly, DR presented a pro-inflammatory profile with expression of CXC and CCL chemokines and was associated with infiltrating neutrophils. Moreover, LPC markers correlated with liver expression and circulating levels of inflammatory mediators. In vitro, human LPC organoids mimicked ductular reaction gene expression profile and produced chemokines. Moreover, LPC promoted neutrophil migration and enhanced their inflammatory profile.   Conclusions: Here we report for the first time the gene expression signature of DR in AH and its association with disease progression. Functional and experimental analysis demonstrates that DR cells have a pro-inflammatory profile, and suggest their involvement in neutrophil recruitment and liver inflammatory response.

overall_design: The genome wide transcriptome of  4 Liver organoids and  4  compensated cirrhotic liver samples  were assessed using Affymetrix HG-U219 genechips (Affymetrix)

first: M

last: Coll

first: B

last: Aguilar

first: J

first: P

last: Sancho


title: Molecular subtype classification of urothelial carcinoma in Lynch syndrome

status: Public on Jan 01 2019

city: Lund

first: Gottfrid

last: Sjodahl

address: Medicon Village

department: Department of Translational Medicine

country: Sweden

institute: Lund Univeristy

summary: We aimed to provide a molecular description of Lynch syndrome-associated urothelial cancer in relation to molecular subtypes of sporadic bladder cancer. Whole genome mRNA expression profiles of 41 tumors and immunohistochemical stainings against FGFR3, KRT5, CCNB1, RB1, and CDKN2A (p16) of 37 tumors from Lynch syndrome patients were generated. Pathological data, microsatellite instability, anatomic location, and overall survival data was analyzed and compared with data from sporadic bladder cancer.

overall_design: 41 tumor samples from the urinary bladder, or upper urinary tract were included. RNA was isolated from macro-dissected FFPE blocks. Gene expression data was normalized, centered and summarized at the gene level. Hierarchical clustering indicates three clusters of Urothelial Lynch syndrome tumors. Molecular subtype classification was performed by a casewise nearest-neighbor (Pearson-r) comparison to a large published dataset on sporadic urothelial bladder cancer generated by the same method and platform as here.

first: Christina

last: Therkildsen

first: Pontus

last: Eriksson

first: Mattias

last: Höglund

first: Patrick

last: Joost

first: Mats

last: Jönsson

last: Sjödahl

first: Mef

last: Nilbert

first: Fredrik

last: Liedberg


title: Impact of CG5694/ova in Drosophila ovaries

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

country: China

institute: NIBS

type: Genome binding/occupancy profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Single Cell RNA-seq for porcine oocytes

status: Public on Jan 17 2019

city: Harbin

first: Zhi-Qiang

last: Du

address: 59 Mucai Street, XiangFang District

institute: Northeast Agricultural University

summary: We report the application of single cell transcriptome sequencing technology for high-throughput profiling of the brilliant cresyl blue test-positive porcine oocytes had higher rates of meiotic maturation, lower death rates, and better cleavage and blastocyst rates as well. Single oocyte transcriptome sequencing on porcine germinal vesicle (GV) stage oocytes that differentially stained by BCB identified 155 genes with significant abundance differences, including CDC5L, LDHA, SPATA22, RGS2, PAIP1, WEE1B and HSP27, which enriched in functionally important signaling pathways, such as spliceosome, cell cycle, oocyte meiosis, and nucleotide excision repair.

overall_design: Assays on three BCB-positive and three BCB-negative GV porcine oocytes.

first: Cai-Xia

last: Yang


title: SAM68 is required for regulation of Pumilio by the NORAD long noncoding RNA

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

summary: The number of known long noncoding RNA (lncRNA) functions is rapidly growing, but how those functions are encoded in their sequence and structure remains poorly understood. NORAD is a recently characterized, abundant, and highly conserved cytoplasmic lncRNA that is required for proper mitotic divisions in human cells. NORAD antagonizes repressors from the Pumilio family that bind at least 17 sites spread through 12 repetitive units  in NORAD sequence. Here we study conserved sequences in NORAD repeats, identify additional interacting partners, and characterize the interaction between NORAD and the RNA binding protein SAM68 (KHDRBS1), which is required for NORAD function in antagonizing Pumilio. The interactions between NORAD, Pumilio and SAM68 provide a paradigm for how specific repeated and structured elements with a lncRNA can facilitate its function.

overall_design: RNA-seq following perturbations of SAM68 in U2OS cells and NORAD lncRNA in HCT116 WT and SAM68 KO cells

first: Ailone

last: Tichon


title: Impact of CG5694/ova on H3K4me2 and pol II patterns in Drosophila ovaries [ChIP-seq]

summary:
Purpose:  To analysis Ova impact on H3K4me2 and pol II patterns in Drosophila ovaries by ChIP-seq
Methods: Chromatin Immunoprecipitation to identify H3K4me2 and pol II patterns in Drosophila ovaries
Results: Knockdown of Ova increases of H3K4me2 and Pol II in some genomic regions.

overall_design: Chromatin Immunoprecipitation H3K4me2 and pol II in w1118(Ctrl) and germline-specific nosGAL4 driven ova RNAi ovaries, followed by deep sequencing analysis.

first: Fu

first: Rongwen

last: Xi


title: HnRNPGT knockout disrupts pre-mRNA splicing and arrests sperm development prior to meiotic metaphase

status: Public on Jan 15 2019

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

country: United Kingdom

institute: Newcastle University

summary: Human male infertility has long been associated with genetic defects that affect nuclear RNA binding proteins, yet what RNA targets these proteins control or why their absence causes infertility remain poorly defined. Here we find that genetic knockout of the mouse nuclear RNA binding protein gene Hnrnpgt causes azoospermia. Knockout male germ cells arrest during the highly transcriptionally active stage of meiotic prophase with altered meiotic nuclear RNA processing patterns. Hnrnpgt knockout most notably leads to the inclusion of previously unidentified cryptic exons that could otherwise disable gene function and poison the meiotic transcriptome. Hnrnpgt target genes include Esco1 and Kdm4d, which encode proteins that are important for chromosome function, and Hnrnpgt null germ cells have altered  centromere clustering and H3K9me3 distribution patterns. Our data reveal a nuclear RNA processing programme that is critical for meiotic metaphase entry.

overall_design: Gene expression profiling by RNA-Seq of mouse testes 18 days post-partum.  Samples from C57BL/6 background, either wild type (n=3) or HnRNPGT Cre-Lox knockout (n=3).

first: Ingrid

last: Ehrmann

first: James

last: Crichton

first: Matthew

middle: R

last: Gazzara

first: Dirk

middle: G

last: de Rooij

first: Jannetta

last: Steyn

first: Ian

last: Adams

first: Yoseph

last: Barash

first: David

last: Elliott


title: Nucleosome Positioning by an Evolutionarily Conserved Chromatin Remodeler Prevents Aberrant DNA Methylation in Neurospora.

status: Public on Jan 16 2019

city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

institute: University of Colorado Colorado Springs

type: Genome variation profiling by high throughput sequencing

summary: Aberrant DNA methylation is often associated with cancers and DNA-demethylating agents such as 5-azacytidine (5-azaC) are often used for anti-tumor therapy. Although it is clinically effective at inhibiting DNA methylation, the mechanistic effect that 5-azaC elicits on eukaryotic cells is controversial. It has been proposed that incorporation of 5-azaC into DNA during replication irreversibly tethers cytosine methyltransferases (MTases) to DNA. This DNA-MTase adduct is targeted by the DNA repair machinery and removed to restore normal DNA functionality; as such some DNA repair mutants are sensitive to 5-azaC. However, double mutants lacking both the cytosine MTase and DNA repair enzymes are still 5-azaC susceptible. Here, we characterize a defective in methylation (dim) mutant of Neurospora crassa, dim-1, that is resistant to 5-azaC when DNA repair is abolished. The causative mutation in a dim-1 strain is in an AAA-ATPase chromatin remodeler conserved from yeast to humans, and indeed a Δdim-1 strain has atypically-spaced nucleosomes within heterochromatic, intergenic, and genic regions, suggesting that DIM-1 influences nucleosome positioning genome-wide. A dim-1 mutant has an ~40-50% reduction in total cytosine methylation but surprisingly gains new cytosine methylation peaks at intergenic regions that are often the promoters of highly expressed genes; nucleosome disorder and DIM-1 localization are also observed at these regions. We propose aberrant nucleosome density not only signals for the catalysis of cytosine methylation in Neurospora, but plays a role in 5-azaC resistance upon loss of DNA repair. Our data shed light on a new relationship between aberrant DNA methylation, DNA repair, an anti-tumor DNA demethylating agent, and nucleosome positioning.

overall_design:
MNase-seq: We analyzed nucleosome positioning by micrococcal nuclease (MNase) digestion followed by paired end sequencing of the mono- and di-nucleosome fractions (as well as the linker DNA) from the 8 and 10 minute timepoints from a MNase timecourse digestion of uncrosslinked, isolated nuclei.
ChIP-seq: We analyzed a dim-1 complete deletion strain (N5801) of Neurospora crassa  by Chromatin Immunoprecipitation for the histone marks H3K9me3, H3K4me3, and H3K27me2me3. Strains were grown, crosslinked, lysed, the histone marks were immunopurified, and associated DNA was sequenced.
RNA-seq: We analyzed a dim-1 complete deletion strain of Neurospora crassa by poly-A+ mRNA-sequencing for gene expression changes by monitoring poly-adenylated messenger RNA levels in duplicate. A wild type strain (N3752) serves as the reference strain (deposited in GSE82222).
Bisulfite-seq: Examination of cytosine methylation, as determined by bisulfite treatment, of two dim-1 strains (a "natural" strain that was the outcome of a mutant selection, and a dim-1 [NCU06484] complete deletion strain). Wild type Bisulfite-seq, deposited in GSE61175, was used as a positive control for comparison

middle: D

first: Miki

last: Uesaka

first: Tereza

last: Ormsby

first: Michael

last: Rountree

first: Elizabeth

middle: T

last: Wiles

first: Keyur

middle: K

last: Adhvaryu

first: Shinji

last: Honda

first: Eric

middle: U

last: Selker


title: Critical function of DNA methyltransferase 1 in tomato development and regulation of the DNA methylome and transcriptome

status: Public on Jan 22 2019

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

summary: DNA methylation confers epigenetic regulation on gene expression and thereby on various biological processes. Tomato has emerged as an excellent system to study the function of DNA methylation in plant development. In contrast to recent discoveries that DNA demethylation is critical for tomato fruit ripening, regulation and function of DNA methylation maintenance remains unclear in tomato plants. Here we report the critical function of tomato (Solanum lycopersicum) Methyltransferase 1 (SlMET1) in plant development and DNA methylome and transcriptome regulation. Using CRISPR-Cas9 gene editing, we generated slmet1 mutants and discovered that SlMET1 is required for normal development of flowers and seeds in tomato. Mutations in SlMET1 caused CG hypomethylation and CHH hypermethylation on a whole-genome scale, leading to a disturbed transcriptome including defects in the expression of key genes involved in meristem formation, seed development and fruit ripening. Consistently, the slmet1 mutants showed impaired flower production, elevated lycopene levels in fruits, and pathenocarpic fruits. In the slmet1 mutants, hypomethylated CG and hypermethylated CHH cytosines are preferentially located in genes and transposable elements (TEs), respectively. Neither the CG hypomethylation nor CHH hypermethylation in the slmet1 mutants is related to tissue culture-induced non-CG hypomethylation, which prefers genes over TEs and is more stable in the former regions than the latter during subsequent inbreeding. Our results depict SlMET1- and tissue culture-dependent tomato DNA methylomes, and that SlMET1 is required for normal development of flowers and seeds, thereby highlighting a role of DNA methylation in determining the yield of normal tomato fruits.

overall_design: MethylC-Seq: 7 samples examined, wtO8, wtR0, slmet1-T0-A, slmet1-T0-B, wtR1, slmet1-1-T1-A, and slmet1-1-T1-B; mRNA-Seq: 3 samples examined, wtR1, slmet1-1-T1-A, and slmet1-1-T1-B (each sample has 2 replicates)

first: Yu

last: Yang

first: Kai

last: Tang

first: Tatsiana

last: Datsenka

first: Huiming

last: Zhang


title: Derivation of hypoblast stem cells from rat embryonic stem cells. [Affymetrix]

city: Minneapolis

first: Dong Seong

last: Cho

state: MN

address: 421 Washington Ave S.E.

department: Chemical Engineering and Materials Science

institute: University of Minnesota

summary:
Hypoblast stem cells were derived from rat embryonic stem cells (rESCs) by culturing with LIF, EGF, PDGF, and 2% fetal bovine serum. mRNA expression profiles of the cells during derivation at different time points were determined with Affymetrix microarrays.
Global transcriptome of rESC-derived hypoblast stem cells (cHypoSCs) was similar to that of rat embryo-derived hypoblast stem cells and rat multipotent adult progenitor cells. In addition, the transcriptome of these cells were compared with the previously published datasets including transcriptome of mouse embryonic stem cells, extraembryonic endoderm cells, single cells of mouse embryos (E3.25, E3.5, and E4.5). The comparison revealed that cHypoSCs have the transcriptome similar to that of extraembryonic endoderm cells and E3.5 primitive endoderm cells.

overall_design: Cells transitioning from rESCs to cHypoSCs (day 0, day 7, day 17, and day 32) were prepared. rESCs grown on feeder-free and feeder-dependent culture were used for derivation of cHypoSCs, and the cells from each condition were used. RNA was extracted from these cells. Then, the samples were hybridized to GeneChip Rat Gene 1.0 ST array (Affymetrix).

first: Dong

middle: S

first: Wei-Shou

last: Hu


title: Derivation of hypoblast stem cells from rat embryonic stem cells.


title: Somatic ACE regulates self-renewal of mouse spermatogonial stem cell via MAPK signaling pathway

city: Nanjing

first: Xiaoyan

last: Huang

address: No.101, longmian Avenue

department: Department of Histology and Embryology

institute: State Key Laboratory of Reproductive Medicine, Nanjing Medical University

summary: To further explore the  mechanism  involved in sACE mediated SSCs proliferation. We established microarray gene expression profiles with or without captopril treatment in cultured SSCs and identified 651 differentially expressed genes (Fold Change>2, P<0.05). Among them, 297 genes were remarkably upregulated and 354 genes were downregulated in three comparison groups after captopril treatment.Then bioinformatical analysis including GO analysis and KEGG pathway analysis were performed and both of them indicated these differentially expressed genes might be involved in regulation of tyrosine phosphorylation of STAT protein, ERK1 and ERK2 cascade, MAPK signaling, Jak-STAT signaling and et al. Four MAPK signaling related genes (Pla2g12b, Cacna2d1, Dusp2, Fgf3) from this signature was quantified  by real-time PCR.

overall_design: Captopril can inhibite the activity of sACE, so 0.01M captopril was added to SSCs culture for 24 hours. SSCs cultured  with 0.01M ddH2O served as Negative control. Three independent experiments were performed .

first: X

first: T

last: Gao

first: B

last: Shao


title: Genome-wide maps of chromatin modifications in a breast cancer cell line

city: Stanford

first: Mark

middle: A

last: Zarnegar

state: CA

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

summary: We report the H3K27ac status in MDA-MB231 breast cancer cells after knockdown of CDK19 and CDK8.

overall_design: Examination of histone marks using a breast cancer cell line transduced with control shRNA or shRNA to knockdown CDK19 and CDK8

first: Robert

middle: W

last: Hsieh

first: Michael

middle: F

last: Clarke


title: Circulating Exosomal miR-20b-5p is Elevated in Type 2 Diabetes and Could Impair Insulin Action in Human Skeletal Muscle.

status: Public on Jan 10 2019

city: Stockholm

first: Mutsumi

last: Katayama

address: Solnavägen 9

department: Physiology and Pharmacology

institute: Karolinska Institutet

summary: MicroRNAs (miRNAs) are noncoding RNAs representing an important class of gene expression modulators. Extracellular circulating miRNAs are both candidate biomarkers for disease pathogenesis and mediators of cell-to-cell communication. We examined the miRNA expression profile of total serum and serum derived exosome-enriched extracellular vesicles in people with normal glucose tolerance or type 2 diabetes. In contrast to total serum miRNA, which did not reveal any differences in miRNA expression, we identified differentially abundant miRNAs in type 2 diabetes patients using miRNA expression profiles of exosome RNA (exoRNA). To validate the role of these differentially abundant miRNAs on glucose metabolism, we transfected miR-20b-5p, a highly abundant exoRNA in type 2 diabetic patients, into primary human skeletal muscle cells. miR-20b-5p overexpression increased basal glycogen synthesis in human skeletal muscle cells. We identified AKTIP and STAT3 as miR-20b-5p targets. miR-20b-5p overexpression reduced AKTIP abundance and insulin-stimulated glycogen accumulation. In conclusion, exosome derived extracellular miR-20b-5p is a circulating biomarker associated with type 2 diabetes, which plays an intracellular role in modulating insulin-stimulated glucose metabolism via AKT signaling.

overall_design:
The purpose of this study was to validate the role of differentially abundant miRNAs on glucose metabolism. We transfected miR-20b, a highly abundant exoRNA in type 2 diabetic patient exosomes, into primary human skeletal muscle cells.
We used microarrays to detail the global regulation of gene expression by miR-20b and identified up- and down-regulated genes by miR-20b in primary human skeletal muscle cells.
To search for target genes of miR-20b, we performed transcriptome analysis to compare expression profiles between human skeletal muscle cells transfected with miR-20b and those transfected with a negative control.

first: Anna

last: Krook


title: MMSET I acts as an oncoprotein and regulates GLO1 expression in t(4;14) multiple myeloma cells

city: Singapore

first: Zhigang

last: Xie

address: 14 Medical Drive, CeLS Building #02-07

department: CSI Singapore

country: Singapore

institute: National University of Singapore

summary: Multiple myeloma (MM) is characterized by recurrent chromosomal translocations. The translocation t(4;14)(p16;q32) is one of the most common translocation in MMs, affecting 15% of patients, and is associated with very poor prognosis. The histone methyltransferase (HMTase) MMSET is universally overexpressed in t(4;14) MM as a result of the t(4;14) translocation. MMSET is capable of producing 3 major isoforms, the full length MMSET II, short isoforms REIIBP and MMSET I. MMSET II has been suggested to play an important tumorigenic role in t(4;14) MM, but little is yet known about whether and how the MMSET short isoforms contribute to MM tumorigenesis. The aim of this study is to characterize MMSET I roles and determine its downstream targets in t(4;14) MM. In t(4;14) MM cells MMSET I knockdown with shRNAs induced cell apoptosis, reduced colony formation and inhibited tumorigenicity in vivo. We also found MMSET I knockdown decreased GLO1 expression, and ectopic MMSET I increased GLO1 expression, suggesting that MMSET I is an upstream regulator of GLO1. Further analysis indicated that MMSET I bound to GLO1 promoter region and depended on its C-terminus to regulate GLO1 expression. Our preliminary data suggested that MMSET I is an oncoprotein and could regulate GLO1 expression in t(4;14) multiple myeloma cells.

overall_design: KMS11 cells were treated with shRNAs for 72 h. Total RNA was extracted by using the Qiagen RNeasy Mini kit (Germany). Gene expression was performed using the GeneChip™ Human Gene 2.0 ST Array (Affymetrix) following the manufacturer’s instructions. Data analysis was performed using GeneSpring software from Agilent Technologies.

first: Chooi

last: Yuan

first: Xie

last: Zhigang

first: Chng

last: Joo


title: Transcriptomic analysis to underly the heterogeneity between 4 cellular models derived from patients diagnosed with pediatric high-grade gliomas under controlled atmosphere (modulation of oxygen level).

city: strasbourg

first: Anne-Florence

last: Blandin

state: bas-rhin

address: 3 avenue molière

department: Hautepierre hospital

country: France

institute: University of Strasbourg

summary: Generation of preclinical models which recapitulate at best the extreme intra-tumoral heterogeneity (using two cell culture conditions) and inter-tumor heterogeneity between children diagnosed with high-grade gliomas.

overall_design: Gene expression modulation was assess by high-throughput RNA sequencing between monolayer and neurosphere cell culture exposed to deprivation of oxygen described in tumor patient versus normal condition (normoxy).

first: Aurélie

last: Durand

first: Natacha

last: Entz-Werle


title: Characterization of a novel OTX2-driven self-renewal program in Group 3 and Group 4 medulloblastoma [expression]

city: Winnipeg

first: Tamra

last: Werbowetski-Ogilvie

state: Manitoba

address: 611-745 Bannatyne Avenue

department: Biochemistry & Medical Genetics

country: Canada

institute: University of Manitoba

summary: Medulloblastoma (MB) is the most common malignant primary pediatric brain cancer. Among the most aggressive subtypes, Group 3 and Group 4 originate from stem/progenitor cells, frequently metastasize, and often display the worst prognosis, yet, as the names imply, we know the least about the molecular mechanisms driving their progression. Here, we show that the transcription factor orthodenticle homeobox 2 (OTX2) promotes self-renewal while inhibiting differentiation in vitro and increases tumor-initiating capacity from MB stem cell populations in vivo. Characterization of the OTX2 regulatory network revealed a novel relationship between OTX2 and genes associated with multiple axon guidance signaling pathways in Group 3 and Group 4 MB stem/progenitor cells. In particular, OTX2 levels were negatively correlated with semaphorin (SEMA) signaling, as expression of 9 SEMA pathway genes is upregulated following OTX2 knockdown with some being potential direct OTX2 targets. Importantly, this negative correlation between OTX2 and SEMA pathway genes was also observed in patient samples, with lower expression of SEMA4D associated with poor outcome in Group 3 and 4 tumors. Functional studies using established and newly derived MB cell lines demonstrated that increased levels of SEMA pathway genes are associated with decreased self-renewal and growth, and that RHO signaling, known to mediate the effects of SEMA genes, is contributing to the OTX2 KD phenotype. Our study provides critical mechanistic insight into the networks controlled by OTX2 in self-renewing MB cells and reveals novel roles for axon guidance genes and their downstream effectors as putative tumor suppressors and therapeutic targets in Group 3 and Group 4 MB.

overall_design: OTX2 knockdown versus scramble control

first: Margaret

last: Stromecki


title: Serotonin signaling via 5-HT3A alters development of sacral neural crest derivatives that innervate the lower urinary tract

status: Public on Dec 31 2018

city: Nashville

first: Yan

last: Guo

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

summary: The autonomic nervous system is derived from the neural crest and supplies motor innervation to the smooth muscle of visceral organs, including the lower urinary tract (bladder and urethra, LUT).  In rodents, autonomic innervation of the LUT is supplied by the major pelvic ganglia (PG) that lie near the neck of the bladder and proximal urethra.  Compared to other autonomic ganglia, the PG are unique in that they harbor both sympathetic and parasympathetic neurons.  The coordinated activity of PG neurons is critical for normal functioning of the LUT – however, surprisingly little is known about how PG neuronal diversity is established or what molecular factors control PG development.  In this study we conducted transcriptome profiling of Sox10-H2BVenus+ sacral neural crest (NC) progenitors to discover candidate genes involved in PG neurogenesis.

overall_design: The long term study goal is to create an encyclopedia of genes that participate in regulating formation of innervation in the lower urogenital tract. Neuronal progenitors that derive from the neural crest have been isolated based on their expression of a Sox10-H2BVenus transgene (C3Fe.Tg(Sox10-HIST2H2BE/Venus)ASout) and their transcriptional profiles determined by hybridization to mouse microarrays with essentially complete genome coverage to quantitate expression levels of genes in FACS isolated populations.

first: E

last: Southard-Smith


title: The REL domain of the NFATc2 protein binding to four types of DNA using protein binding microarrays

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

summary: NFATc2 is a sequence specific DNA binding protein in the Rel family that binds a 5-mer motif CGGAA better when both cytosines in the CG dinucleotide are methylated.  Using protein binding microarrays (PBMs) we examined the DNA binding of NFATc2 to three additional types of DNA: (1) single-stranded DNA (ssDNA), (2) double stranded DNA (dsDNA) with 5-methylcytosine (5mC, M) in one strand and cytosine in the second strand (dsDNA(5mC|C)) and (3) DNA with 5-hydroxymethylcytosine (5hmC, H) in one strand and cytosine in the second strand (dsDNA(5hmC|C)).  NFATc2 binding to ssDNA is strongest for the 7-mer ATTTCCA.  While NFAT can bind ssDNA, the average binding to the 40,000 DNA features of the PBM was twice as high for ssDNA compared to dsDNA, with maximal binding observed to dsDNA, suggesting that NFAT binding to dsDNA is more specific.  dsDNA sequences containing the 5-mer MGGAA with 5mC in one DNA strand are better bound than CGGAA, with methylation of a single cytosine being sufficient for the stronger binding seen when both cytosines in the CG dinucleotide are methylated.  Several DNA sequences containing HGGAA are also better bound than those containing cytosine, however the effect of 5hmC is not as dramatic as that of 5mC.   Analysis of available NFATc2:DNA complexes rationalizes our PBM data.

overall_design: Protein binding microarray (PBM) experiments were performed for the Rel domain of human NFATc2. Briefly, the PBMs involved binding of N-terminal GST-tagged NFATc2 Rel domain to single stranded or double-stranded 44K Agilent microarrays (Berger et al., Nature Biotechnology 2006) in order to determine its binding preferences to sequences containing unmodified and modified cytosines.  We modified the double stranding step of the PBM protocol in which the nucleotide mixture contained 5-methylcytosine or 5-hydroxymethylcytosine.  Details of the modified cytosine PBM protocol are described in Khund-Sayeed S et al., Integrative Biology, 2016.


title: Characterization of a novel OTX2-driven self-renewal program in Group 3 and Group 4 medulloblastoma


title: Nucleolar DNA

city: Rochester

first: jinlong

last: lu

state: NY

address: 213 Hutchinson Hall

institute: University of Rochester

summary: The nuclear organization and location of genes in metazoan organisms is not random. Functionally  DNA elements or DNA regions residing on different chromosomes may  reside in specific nuclear compartments and stay closely in 3D space. Nucleolus is the largest nuclear compartment and we aim to explore what kind of genomic fractions locate in it.

overall_design: All DNA-seq(s) were designed to reveal the nucleolar fraction of genomic DNA .

first: Wen

last: Shao

first: Xiaohua

last: Shen


title: Identification of Latrophilin-2, a Specific Cell-surface Marker for Cardiac Progenitor Cells, and its Functional Significance in Heart Development [RNA-Seq]

city: Seoul

first: Choon-Soo

last: Lee

address: 28 Yongon-Dong, Jongno-gu

country: South Korea

institute: Seoul National University Hospital

summary:
Background: Identification of a lineage-specific marker plays a pivotal role in understanding developmental process and is necessary to isolate a certain cell type with high purity for therapeutic purposes. Here, we report a new cardiac-specific marker and demonstrate its functional significance in cardiac development.
Methods: When mouse pluripotent stem cells (PSCs) were stimulated with BMP4, Activin A, and bFGF, they differentiated into cardiac cells. To screen molecules expressed on cardiac progenitor cell (CPC) surfaces compared to those on undifferentiated PSCs, we isolated Flk1+/PdgfRa+ cells at differentiation day 4 and performed microarray analysis.
Results: Among candidates, we identified a new G protein-coupled receptor, latrophilin-2 (Lphn2). Here, we report this new cardiac-specific surface marker, Lphn2, expressed specifically on CPCs and cardiomyocytes (CMCs) during mouse and human PSC differentiation in vitro and exclusively in the heart during mouse embryonic development. Lphn2 knockout in mice was embryonically lethal because of severe heart, but not vascular, defects. PSC-derived Lphn2+ cells, but not Lphn2- cells, differentiated into CMCs and regenerated the myocardium when transplanted into infarcted hearts. Transplanted Lphn2+ cells improved left ventricular systolic function and reduced infarct sizes. Analysis of the signaling pathway indicated that cyclin-dependent kinase 5 is downstream of Lphn2 and collaborates with Src kinase to induce P38MAP kinase phosphorylation, subsequently activating cardiac-related gene transcription.
Conclusion: Lphn2 is a functionally significant cell-surface marker for cardiac progenitor and cardiomyocytes. These findings provide a valuable tool for isolating cardiomyogenic progenitors and CMCs from PSCs and shed light on heart development and regeneration.

overall_design: 6 samples are analyzed by 2 groups

first: Hyun-Jai

last: Cho

first: Jin-Woo

first: Jaewon

first: Yoo-Wook

last: Kwon

first: Hanseul

last: Park

first: Jongpil

last: Kim

first: Hyo-Soo


title: Genome-wide profiling of circular RNAs in rapidly growing culms of moso bamboo

city: fuzhou

first: Lianfeng

last: Gu

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

institute: Fujian Agriculture and Forestry University

summary: Transcriptome analysis of circular RNAs in the fast-growing species moso bamboo

overall_design: Circular RNAs (circRNAs) are new type of the noncoding RNAs that are stable and broadly expressed in mammalian. Moso bamboo represents one of the fast growth plants in the world. To better understand the potential function of circRNAs in developing culms, we performance genome-wide identification of differential circRNAs using high through sequencing of rRNA-depletion samples on eight different developmental stages of culm material. We focus on identification of circRNAs associated with internode elongation. Additionally, circRNAs function as miRNA sponges and regulation of their corresponding parental genes in developing culms were studied using small RNA sequencing and strand-specific RNA-seq. Taken together, this study of circRNAs in moso bamboo culm at different stages provide further information about the new research hotspot of long non-coding in plant.

first: Yongsheng

last: Wang


title: Resolving Cell Fate Decisions during Somatic Cell Reprogramming by Single-Cell RNA-seq

city: Guangzhou

first: Lihui

last: Lin

state: Guangdong

address: No.190, Kaiyuan Street

department: Stem cell

institute: Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science

summary: The use of Yamanaka factors or chemical compound converting mouse embryonic fibroblasts (MEFs) into induced pluripotent stem cells (iPSCs). However, these reprogramming processes are highly heterogeneous and remain poorly understood. Here we comprehensively profile the different stages of an optimized Oct4, Sox2, Klf4 and chemical-induced reprogramming at single-cell resolution.

overall_design:
Using high efficient OSK induced reprogramming systems, which can get chimera-competent iPSCs at D7, we collected cells across 8 days reprogramming time course [1] using Fluidigm C1. In total, we analyzed 912 single cells isolated at D0, D1, D2, D3, D5, D7, D8, plus MEFs, iPSCs, and ESCs were sequenced, [2] using 10x Genomics, we analyzed 59141 single cells after QC isolated at D0, D1, D3, D5, D6, D7, D8, plus MEFs and ESCs (GSM3629847-GSM3629855).

Using chemical induction of pluripotency (CIP) systems, we collected cells across 40 days reprogramming time course using 10x Genomics (GSM3619570-GSM3619581). In total, we analyzed 93585 single cells after QC isolated at D0, D3, D6, D9, D12, D16, D18, D22, D26, D32, D36, D40.

first: Jeikai

last: Chen

first: Duanqing

last: Pei


title: Endothelial progenitor cells contribute to neovascularization of non-small cell lung cancer via HDAC7 mediated cytoskeleton regulation and angiogenic genes transcription

city: Wuhan

first: Ye

last: Wei

state: Hubei

address: Tongji Medical College, Huazhong University of Science and Technology

institute: Cancer Center, Union Hospital

summary:
To supply tumor tissues with nutrients and oxygen, endothelial progenitor cells (EPCs) are recruited to tumor bed and contribute to tumor neovascularization.  HDAC7 is a critical regulator in EPC-mediated neovascularization.
To explore the function of HDAC7 in neovascularization induced by EPCs, we use microarrays to profile the genes expression changes in HDAC7 lacking EPCs. HDAC7 silencing upregulated antiangiogenic genes transcription and suppressed proangiogenic genes expression, turning off the angiogenic switch for vessel formation.

overall_design: EPCs were isolated from human umbilical cord blood of healthy volunteers and the 3rd passage of cultured EPCs were selected for lentivirus infection.  EPCs isolated from the same volunteer were devided into KD and NC group. EPCs were infected with lentivirus carrying HDAC7 shRNA in KD group and nonspecific random shRNA in NC group. Each group contains 2 samples from different volunteers for RNA extraction and  hybridization on Affymetrix microarrays.

first: Fangzheng

last: Zhou

first: Haibo

first: Jing

last: Huang

first: Dandan

last: Yu

first: Gang

last: Wu


title: Single cell functional genomics reveals the importance of mitochondria in cell-to-cell phenotypic variation

city: Barcelona

first: Riddhiman

last: Dhar

state: Barcelona

address: C/ Dr. Aiguader, 88

department: EMBL-CRG Systems Biology Program

institute: Centre for Genomic Regulation

summary: Yeast cells were stained with TMRE, which measures mitochondrial membrane potential, and were sorted onto four bins - HI,M1,M2 and LO, from TMRE vs cell-size plot. Total RNA was isolated from cells and RNA sequencing was done to compare transcriptome profile in sub-population of cells that differ in mitochondrial membrane potential. Cells with high potential showed repression of respiration genes, exhibited signs of DNA damage and iron deficiency.

overall_design:
Transcriptome comparison of yeast sub-populations that differ in mitochondrial membrane potential
mitochondrial membrane potential HI> M1> M2> LO
bin T1=bin HI
bin T2=bin M1
bin T3=bin M2
bin T4=bin LO

first: Alsu

last: Missarova

first: Ben

last: Lehner

first: Lucas

middle: B

last: Carey


title: Profiling of T. brucei rRNA Nm landscape using RibOxi-seq

city: Farmington

first: Gordon

middle: G.

last: Carmichael

state: CT

address: 263 Farmington Avenue

department: Genetics and Genome Sciences

institute: UConn Health

summary: We performed RiOxi-seq on both procyclic form and bloodstream form of T. brucei in order to contribute to the extensive characterization of 2'-OMe sites by Dr.Michaeli's lab and collaborators.

overall_design:
Total RNAs were extracted and experiments were performed according to RibOxi-seq protocol
Sequencing data were subsequently analyzed according to RibOxi-seq protocol

first: Yinzhou

last: Zhu

first: Ankita

last: Srivastava

first: Arthur

last: Gunzl


title: PSORITUS - Secukinumab study in PSOriasis exploring pruRITUS intensity and lesional biomarkers (CAIN457ADE03)

city: muenster

first: karin

last: loser

state: nrw

address: von-esmarch-str. 58

department: dermatology

country: Germany

institute: university of muenster

summary:
Exploratory study on the kinetics of psoriasis symptoms, pruritus intensity and lesional biomarkers in patients with moderate to severe plaque-type psoriasis treated with subcutaneous
secukinumab (300 mg) during a 16 week open-label run-in phase followed by a 16 week randomized, double-blind, placebo-controlled withdrawal phase.

overall_design: Psoriasis patients received 300 mg subcutaneous secukinumab during a 16 week open-label run-in phase followed by 16 week randomized, double-blind, placebo-controlled withdrawal phase

first: S

last: Ständer

first: M

last: Franz

first: N

last: Melzer

first: C

last: Siedler

last: Pruckner

first: K

last: Loser


title: Long-term intermittent fasting restores function of the gut–liver axis and prevents development of diabetic retinopathy in db/db mice

city: Indianapolis

first: Leni

last: Moldovan

address: 980 W Walnut St., Rm. C422

department: Ophthalmology

institute: Indiana University

summary: Constant availability of food can contribute to the pathogenesis of metabolic syndrome and type 2 diabetes. Short term intermittent fasting (IF) can reset the central, light-entrained (suprachiastmatic nucleus) clock and also the peripheral, food-entrained (liver) clock to restore metabolic homeostasis in T2D. We asked if long term IF could prevent development of diabetic retinopathy (DR) in a type 2 diabetes model, the db/db mouse. After 7 months, IF corrected diabetes-induced increases in triglycerides, cholesteryl esters and diglycerides. IF protocol in db/db mice also prevented development of DR. In addition, host frequency and time of food intake affected the gut microbiome composition. IF led to decreased levels of Clostridiales and Akkermansia muciniphila in db/db mice and these changes in flora were accompanied by increased gut mucin, goblet cell number and villus length. Increased levels of Firmicutes in db/db mice on IF supported improved bile acid metabolism. To confirm that the restoration of bile acid function could contribute to the beneficial effects induced by IF on DR, the dual FXR/TGR-5 agonist INT-767 was administered to a second diabetes model, DBA2J mice injected with streptozotocin (STZ) and placed on Western diet (WD). In this model, INT-767 prevented development of DR. These findings support the concept that long-term IF mediates multiple beneficial effect by restoring the gut-liver axis homeostasis.

overall_design: Liver samples from 3 db/db mice per group  were collected at zeitgeber (ZT) time ZT9 (daytime) and ZT21 (nighttime) from both the diabetic ad-lib and IF groups and were used for microarray analysis. Total RNA was extracted using miRNeasy Mini kit (Qiagen, Valencia, CA) and standard procedures were used for hybridization, staining and scanning GeneChip® Mouse Gene 2.0 ST Arrays (Affymetrix, Santa Clara, CA). CEL files were analyzed with Expression Console software (Affymetrix) and the statistical analysis was performed with Transcriptome Analysis Console (Affymetrix) and in R (version 2.15.3). A linear model with covariates of long-term IF effect, ZT time effect and feeding/fasting effect was built and the goodness of fit between the full model and null model was tested by likelihood ratio test. False discovery rate (FDR) correction was conducted to adjust for multiple testing. In this study, the genes with FDR less than 0.3 was selected for further post hoc analysis. Only genes with p values for the comparasion between long term IF treatment and ad-lib less than 0.05 and absolute fold-change larger than 1.5 were selected as statistically significantly expressed genes.

first: Yuanqing

last: Yan

first: Eleni

last: Beli

first: Tatiana

middle: E

last: Salazar

first: Ashay

last: Bhatwadekar

first: Ruli

last: Gao

first: James

last: Dominguez

first: Matthew

last: Richardson

first: Dung

middle: V

last: Nguyen

first: Rehae

middle: C

last: Miller

first: Qi

last: Wang

first: Shakir

middle: H

last: Hindi

first: Harkeerat

last: Dhami

first: Yaqian

last: Duan

first: Todd

last: Lydic

first: Jared

last: Smith

first: Joshua

last: Thomas

first: Emily

last: Hutchinson

first: Fletcher

last: White

first: Sergio

last: Caballero

first: Steven

last: Townsend

first: Luisa

last: Chan

first: Caitlin

middle: N

last: Ryan

first: Daniel

last: Morton

first: Emil

first: Fang-I

last: Chu

first: Gavin

middle: Y

last: Oudit

first: Hartmut

last: Derendorf

first: Luciano

last: Adorini

first: Xiaoxin

first: Michael

last: Boulton

first: Mervin

last: Yoder

first: Moshi

last: Levi

first: Qiuhong

last: Li

first: Julia

last: Busik

first: Maria

last: Grant


title: DYRK2 stabilization has dual effects on apoptosis and self-renewal of leukemia stem cells that can be targeted in chronic myeloid leukemia

city: Houston

first: Toni-Ann

last: Mistretta

state: TX

address: 1 Baylor Plaza, BCM 315

department: Pathology

institute: Baylor College of Medicine

summary:
Gene expression analysis of leukemic stem cells (LSC) from WT and KLF4-deficient BCR-ABL p210-induced chronic myeloid leukemia (CML) mice
Loss of Klf4 impairs self-renewal and survival of LSC in CML. Analysis provides insight into function of KLF4 in leukemia.

overall_design: BCR-ABL p210+ lineage- Sca-1+ c-Kit+ (GFP+ LSK) cells were sorted from WT and Klf4 deficient CML mice induced by BCR-ABL p210 at 14 days after transplantation. Sorted cells were subjected to gene expression analysis.

first: Chun-Shik

last: Park

first: Ye

last: Shen

first: Andrew

last: Lewis

first: Koramit

last: Suppipat

first: Julie

last: Tomolonis

first: Monica

last: Puppi

first: Taylor

last: Chen

first: Paul

last: Peng

last: Mistreta

first: Leyuan

last: Ma

middle: R

last: Green

first: H

last: Lacorazza


title: Genome-wide identification of RD26 target genes

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

institute: MPIMP

summary:
Global transcriptome patterns were determined in 2-week-old RD26-IOE seedlings after 2h (one biological replicate) or 5h (two biological replicates) estradiol (EST) or ethanol (mock) treatment.
EST-induced expression of RD26.

overall_design: To identify genes rapidly responding to elevated RD26 expression, gene expression profiling was performed using Affymetrix ATH1 microarrays.

first: Iman

last: Kamranfar

first: Bernd

last: Mueller-Roeber


title: Developing the gene expression of glomerulus in anti-Thy1 nephritis

city: Beijing

first: Yang

last: Lu

address: 8th fuxing road

institute: PLA general hospital

summary: we followed the course of anti-Thy1 nephritis from days 1 to 5, establishing gene expression profiles at each timepoint using microarrays to explore the development of immunity.

overall_design: We established anti-Thy1 model by injection of anti-Thy1 antibody. The models were killed from day 1 to 5. The normal control group was killed at day 0.  Three glomeruli of each of six rats per timepoint were subjected to microarray analysis.

first: Lei


title: Diet-induced changes in gene expression of lean and obese mice in three different brain regions

first: Ilario

last: De Toma

address: Carrer del Dr. Aiguader, 88

institute: Center for Genomic Regulation

summary: By looking at the transcriptome of the hypothalamus, frontal cortex and striatum, we studied how the fine balance between the homeostatic and hedonic control of food intake can be influenced by diet

overall_design: For 8 weeks, lean group mice had access to standard chow (SC) mouse diet and obese group mice had a free choice access to SC and a chocolate-mixture diet (CM). Fontal cortex, striatum and hypothalamus, from lean and obese groups, were dissected upon completion of an 11-day test battery and total RNAs extracted.

first: Ilona

last: Grabowics


title: Cell surface polysaccharides of Bifidobacterium induce functional regulatory T cells

city: Pohang

first: Gi-Cheon

middle: careful

last: Kim

state: Hyoja-dong Namgu

address: POSTECH, postech biotech center Rm 430, Hyoja-dong Namgu, pohang

institute: IBS

summary: To characterize the effect of CSGG in dendritic cell phenotypic changes, we performed gene expression RNAseq analysis for Mock and CSGG treated splenic dendritic cells after 0h, 4h and 8h of CSGG treatment.

overall_design: Total RNA was extracted from splenic dendritic cells of mock and CSGG treated group.

first: Ravi

last: Verma

first: Chang-hon

last: Lee

first: Eunji

last: Jun

first: Jaeu

last: Yi

first: Kwang-soon

first: Sin-Hyeog

last: Im


title: RNA-Seq Analysis of Spleen from Chicken and Japanese Quail infected with Lentogenic and Velogenic Newcastle Disease Virus

city: University Park

first: Suresh

middle: Varma

last: Kuchipudi

state: PA

address: Animal Diagnostic Laboratory, Wiley Lane

department: Veterinary and Biomedical Sciences

institute: The Pennsylvania State University

summary: Newcastle disease (ND) affects a few hundred avian species including chicken, and the clinical outcome of Newcastle disease virus (NDV) infection ranges from mild to severe fatal disease depending on the NDV pathotype and the host species involved. Japanese quails serve as natural reservoirs of NDV and play important role in NDV epidemiology. While infection of chicken with velogenic NDV results in severe often fatal illness, the same infection in Japanese quails is results in in apparent infection. The molecular basis of this contrasting clinical outcomes of NDV infection is not yet known. We compared global gene expression in spleens of chicken and Japanese quails infected with a lentogenic or velogenic NDVs. We found contrasting regulation of key genes associated with NF-κB pathway and T-cell activation between chicken and Japanese quails. Our data suggests association of NDV resistance in Japanese quails to activation of NF-κB pathway and T cell proliferation.

sample_organism:
Gallus gallus
Coturnix japonica

platform_organism:
Gallus gallus
Coturnix japonica

overall_design: RNA extracted from pools of spleens (n=6) from chickens or Japanese quail infected with Newcastle disease virus (LaSota or 2K3 strain) or mock-infected were analyzed by Illumina RNA-Seq and mapped to the Gallus gallus genome (Galgal4).

first: P

middle: M

last: Kumar

first: Kanagaraj

last: Vijayrani

first: Kathaperumal

last: Kumanan

first: Ruth

last: Nissly

first: Janet


title: Differential expression of genes in the respiratory tree of sea cucumber (Apostichopus japonicus) under normal dissolved oxygen and hypoxia conditions

city: Qingdao

first: Lina

last: Sun

address: Nanhai Road 7

institute: Institute of Oceanology, Chinese Academy of Sciences

summary: The sea cucumber Apostichopus japonicus is a deposit-feeder and vital for marine benthic ecosystems. Hypoxia lasting for several days can lead to massive mortality in A. japonicus. It is important to understand the molecular responses of A. japonicus when exposed to acute changes in DO concentration. In the present study, RNA-seq provided a general overview of the gene expression profiles of the respiratory tree of A. japonicus exposed to dissolved oxygen (DO) of 8 mg/L (DO8), 4 mg/L (DO4) and 2 mg/L (DO2) conditions.

overall_design: One group of sea cucumbers was maintained as the control group with high DO water (DO8) at around 8 mg/L, whereas the other two groups were kept in sea water with nitrogen aeration where the DO concentration gradually decreased to approximately 4 mg/L DO (DO4) and 2 mg/L DO (DO2), which is defined as hypoxia, and they were maintained for 3 days.

first: Libin

last: Zhang


title: Ternary protein•drug•RNA interface explains RocA sequence selectivity and Aglaia resistance

status: Public on Dec 30 2018

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: S205 Bioscience Bldg. 2-1 Hirosawa

department: Cluster for Pioneering Research

country: Japan

institute: RIKEN

summary: A novel class of translation inhibitors isolated from Aglaia plants, exemplified by Rocaglamide A (RocA), shows promise as an anti-cancer therapy. RocA converts its molecular target, translation initiation factor 4A (eIF4A), a DEAD-box protein, into a purine-selective RNA-binding protein that represses protein synthesis from a subset of mRNAs. This unusual mechanism of action raises the question of how the drug induces selectivity for polypurine sequences. Furthermore, as eIF4A is found in all eukaryotes, it is unclear how Aglaia resists the effects of RocA. Here, we assembled the Aglaia transcriptome de novo and identified highly specific mutations in eIF4A that enable it to evade RocA-dependent translation inhibition. Furthermore, we determined the crystal structure of the human eIF4A1•ATP analog•RocA•polypurine RNA complex. RocA binds residues mutated in Aglaia and intercalates between consecutive purines at a sharp RNA bend, revealing the structural basis of polypurine-selective translational inhibition by RocA in human and resistance in Aglaia.

overall_design: Ribosome,profiling

first: Wakana

first: Mari

last: Takahashi

first: Stephen

last: Floor

last: Mito

first: Takuhiro

last: Ito

first: Nicholas

middle: T

last: Ingolia


title: GmRAV1 regulates regeneration of root and adventitious buds by cytokinin in Arabidopsis and soybean

city: Hangzhou

first: Kexin

address: No.9, Meiling South Road

institute: Tea Research Institute,Chinese Academy of Agricultural Science

summary:
Purpose:  The goals of this study are to identify what gene GmRAV1 was related to. RNA-Sequencing experiments were designed between GmRAV1-ox soybeans and DN50 soybeans.
Methods:  Leaves mRNA  of 30-day-old DN50 and GmRAV1-ox soybeans were used by RNA sequencing using Illumina HiSeqTM2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Genome_build: Glycine max Wm82.a2.v1
Results: RNA-seq data confirmed that there are 1467 genes with significant differences. Some genes expression of cytokinin and auxin signaling pathways is dramatically changed, such as GmARR9, GmAUX22, GmPIN1, GmCycD3 and GmPDV2.
Conclusions: GmRAV1 are related to cytokinin and auxin signaling pathways.

overall_design: High-throughput sequencing using Illumina HiSeq 2000 (RNA-Seq) was performed on 30-day-old DN50 and GmRAV1-ox soybeans.

first: Lin

last: Zhao

first: Wenbin

last: Li


title: How the mtDNA load at the beginning of tumorigenesis affects tumourigenesis

city: Clayton

first: Justin

last: St. John

state: Vic

address: 27-31 Wright St

department: Centre for Genetic Diseases

institute: Hudson Institute of Medical Research

summary:
To determine how the mtDNA load at the beginning of tumorigenesis affects the DNA methylation patterns of TRFs during tumourigenesis.
Different loads of mtDNA at the beginning of tumourigenesis have limited impact on the copy number variation contributing to tumorigenesis.

overall_design: GBM tumors formed from HSR-GBM1 cells with four different loads of mtDNA:100%, 50%, 3% and 0.2%.  3 biological replicates of each condition.

last: St John

first: Xin

first: Melinda

last: Ziino


title: RNA sequencing of leaf tissues from two contrasting chickpea genotypes reveals mechanisms for drought tolerance

city: Bundoora

first: Nitin

last: Mantri

state: Victoria

address: Plenty Road

department: School of Science

institute: RMIT University

summary: In this study, the leaf tissue from shoots apical meristem stage of drought tolerant (ICC8261) and drought sensitive (ICC283) genotypes were analyzed using RNA sequencing to identify genes/pathways associated with drought tolerance/sensitivity in the both genotypes. It was observed that genes related to ethylene response, MYB-related protein, xyloglucan endotransglycosylase, alkane hydroxylase MAH-like, BON-1 associated, peroxidase 3, cysteine rich and transmembrane domain, vignain and mitochondrial uncoupling were specifically up-regulated in the tolerant genotype whereas, same genes were down-regulated in sensitive genotype.

overall_design: In our present study, RNA sequencing was employed to identify drought-responsive genes in chickpea leaf tissue of two genotypes ICC8261 and ICC283 to identify biological, cellular and molecular pathways related to drought tolerance under drought stress. The significant difference observed between the two genotypes in shoot apical meristem leaves indicates how drought stresses affect the different mechanisms in both genotypes. In this study the emphasis was on how the regulation of transcription factors and phytohormone signalling transcripts were influenced by drought stress in the two genotypes

first: Sapna

last: Badhan

first: Vijay

last: Bhaskarla

first: Parvas

last: Kole

first: Adrew

last: Ball


title: SCL establishes a global repressive environment and cooperates with Polycomb RYBP-PRC1 to suppress alternative lineages in blood-fated cells [ChIP-seq]

status: Public on Dec 27 2018

city: Oxford

first: Hedia

last: Chagraoui

address: john radcliffe hospital headley way headington

department: Molecular Hematology Unit

institute: Weatherall Institute of Molecular Medicine

summary: Understanding the molecular basis of cell fate decision is critical to shed light onto biological processes supporting tissue formation. In particular, whether lineage-fated cells derive from multi-primed progenitors and need to establish active fate restriction mechanisms to engage in a differentiation pathway is still matter of debate. To characterise the mechanisms underlying specification of blood-fated cells from mesodermal precursors, we studied the transcriptional activity of the key hematopoietic regulator SCL/TAL1. Scl-null mouse embryos die at embryonic day E9.5 from absence of blood formation, and exhibit mis-specification of mesodermal cells into cardiomyocytes, thus offering an excellent entry point for mechanistic studies of fate determination. Using high-throughput assays from mouse ES cell-derived mesodermal cells, we showed that, in parallel with activating the blood program and repressing the cardiac and paraxial programs, SCL strongly activates expression of repressors, such as ETO2 (known partner of SCL) and RYBP (member of Polycomb repressive complex PRC1). ETO2’s association with chromatin reflects SCL’s overall genomic binding, pointing to ETO2’s modulatory, rather than purely repressive, transcriptional activities. In contrast, SCL/RYBP chromatin co-occupancy is preferentially enriched at genes normally repressed in blood-fated cells and involved in early developmental processes and alternative lineages, highlighting a relationship between SCL and RYBP/PRC1 in repressive processes. Remarkably, SCL is critical for maintaining high levels of PRC1-associated repressive histone mark H2AK119ub genome-wide. It is also required for maximal levels of repressive mark H3K27me3 on genes normally repressed. Finally, Rybp knock-down in differentiating ES cells phenocopies the cardiac phenotype of Scl-null cells, supporting a functional interaction between SCL and a critical repressive chromatin remodeling complex. Altogether, these data unveil the establishment of a repressive environment in mesodermal progenitors by a hematopoietic-specific transcriptional regulator. This leads to restriction of expression of regulators of alternative fates and uncompromised commitment towards a hematopoietic identity.

overall_design: mcherry+ cells from D4 EBs were sorted from Scl-mcherry reporter cell lines expressing either wild type SCL (Scl:mcherry) or basic helix-loop-helix deleted, non-functional SCL protein (Scl d/d:mcherry). Mouse mcherry positive sorted cells were mixed in 2:1 ratio to drosophila S2 cell line. Once the mouse and drosophila cells were combined, the sample was treated as a single Chipseq sample throughout the experiment to completion of DNA sequencing. Standard Chip was then carried out and histone/DNA complexes were isolated with the antibodies listed below.

first: Catherine

last: Porcher


title: SCL establishes a global repressive environment and cooperates with Polycomb RYBP-PRC1 to suppress alternative lineages in blood-fated cells [RYBP ChIP-seq]

overall_design: SCL Chip sequencing was performed from two independent wild type ES cell differentiation where we isolated at day 3.75 of EB formation FLK1+ PDGFRa- mesodermal cells.


title: SCL establishes a global repressive environment and cooperates with Polycomb RYBP-PRC1 to suppress alternative lineages in blood-fated cells

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

overall_design: Refer to individual Series


title: Fatty Acid Oxidation and Glycolysis Regulate Skin ECM Homeostasis by Shifting Fibroblasts between Catabolism and Anabolism (BeadChip)

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

institute: Princess Margaret Cancer Centre

summary:
Transcriptome profiling of human radiation-induced skin fibrosis and normal age matched control revealed a shift from catabolic to anabolic pathways in fibrosis.

The paper has been published: https://www.nature.com/articles/s42255-018-0008-5?WT.feed_name=subjects_metabolism

overall_design: HT-12 array profiling of normal and fibrotic human neck skin.

first: Fei

last: Liu


title: Tumor suppressor miRNA inhibits medulloblastoma growth and sensitizes vincristine and radiation response by inducing spindle defects and DNA damage

status: Public on Dec 26 2018

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: Medulloblastoma (MB) is the most common malignant brain tumor in children. Despite recent improvements in overall survival, only a modest percentage of patients survive high-risk MB. The devastating side effects of radiation and chemotherapy substantially reduce qualify of life for surviving patients. We identified a novel tumor suppressor miRNA that sensitizes both ionizing radiation and vincristine responses in medulloblastoma.  To understand the mechanism by which the tumor suppressor miR-584-5p may act as a tumor suppressor and therapy sensitizer, we performed microarray analysis in D425Med and D458Med medulloblastoma cells transfected with scrambled (miR-NC) or miR-584-5p mimic (miR-584-5p).

overall_design: miRNA knockdown experiment with two MB cell lines

first: Nourhan

last: Abdelfattah

first: Subbarayalu

last: Panneerdoss

first: Manjeet

last: Rao


title: Homo sapiens whole blood infected with Candida spp. (here: Candida parapsilosis)

city: Jena

first: Philipp

last: Kämmer

address: Adolf-Reichwein-Straße 23

department: Microbial Pathogenicity Mechanisms

institute: Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI)

summary: Homo sapiens fresh whole blood was infected with Candida parapsilosis. RNA-pool of both species extracted at 0min (control), 15, 30, 60, 120, 240 min. Samples are rRNA depleted. Measurement of Homo sapiens gene expression.

sample_organism:
Candida parapsilosis
Homo sapiens

platform_organism:
Candida parapsilosis
Homo sapiens

overall_design: Examination of three biological replicates for each of the 6 time points.

first: Sylvie

last: McNamara

first: Sascha

last: Brunke

first: Jörg

last: Linde


title: Fatty Acid Oxidation and Glycolysis Regulate Skin ECM Homeostasis by Shifting Fibroblasts between Catabolism and Anabolism

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

The paper has been published: https://www.nature.com/articles/s42255-018-0008-5?WT.feed_name=subjects_metabolism

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Homo sapiens whole blood infected with Candida spp. (here: Candida albicans)

summary: Homo sapiens fresh whole blood was infected with Candida albicans SC5314. RNA-pool of both species extracted at 0min (control), 15, 30, 60, 120, 240 min. Samples are rRNA depleted. Expression measurement of Homo sapiens genes.

sample_organism:
Candida albicans
Homo sapiens

platform_organism:
Candida albicans
Homo sapiens


title: Gene expression profiling induced by electron and proton irradiation in breast cancer cells

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

country: Italy

institute: IBSBC CNR

summary: Radiation therapy (RT) remains a vital component of the curative multimodality therapy for many types of cancer including breast cancer (BC) disease. Thus, many efforts from research teams are needed to help clinicians in understanding the molecular portrait of a specific cancer type. Moreover, technological advances in RT are evolving with the use of hadrons, such as protons. However, cell and molecular changes induced by proton exposure are poorly characterized as well as molecular differences induced by high and low Linear Energy Transfer (LET) irradiation modalities, representing a topic of radiobiological interest. We analyze and compare molecular responses, in term of gene expression profile (GEP) changes, induced by conventional and non conventional radiation treatment modalities characterized by different LET values (using electron and proton beams respectively), delivering the same dose of IR, in tumorigenic and non-tumorigenic breast cell lines.  We trust that this study could have a role in driving RT towards personalised treatments, evaluating possible combined treatments, based also on the molecular characterization in BC.

overall_design: Changes in gene expression in non- tumorigenic MCF10A breast epithelial cell line and in tumorigenic MCF7 and MDA-MB-231 breast cancer cell lines, exposed to 9Gy of electron or proton irradiation, were analyzed as two-color hybridizations using Agilent Technologies whole human genome 4x44K microarrays. Samples were named as follow: MCF10A_9Gy_electron; MCF7_9Gy_electron; MDA-MB-231_9Gy_electron; MCF10A_9Gy_proton; MCF7_9Gy_proton; MDA-MB-231_9Gy_proton.


title: Expression data from human umbilical vein endothelial cells(HUVECs) undergoning normal, hypoxia/reoxygenation-induced injury and Inulin-type oligosaccharides administration

city: Zhengzhou

first: Xuexiang

last: Cha

state: Henan

address: Kexue Avenue 100

department: Basic Medical Science

institute: Zhengzhou University

summary: To characterize the differentially expressed genes in HUVECs between normal, hypoxia/reoxygenation-induced injury and  Inulin-type oligosaccharides administration. Performing the Affymetrix Human Transcriptome Array 2.0 (HTA2.0, n=3) assay demonstrated that Hex5 exposure up-regulated genes enriched in cell cycle progression, DNA replication and repair, ubiquitin-mediated proteolysis, apoptosis, MAPK, and the IP3K-mTOR signaling pathway. Our results suggested that inulin-type oligosaccharides from the root of M.officinalis may protect against H/R-induced tissue injury

overall_design: The Affymetrix Human Transcriptome Array 2.0 (HTA2.0) assay  suggested that Inulin-type oligosaccharides extracting from Morinda officinalis protect human umbilical vein endothelial cells from hypoxia/reoxygenation-induced injury. Each sample had 3 biological replicates

first: Cha

last: Xuexiang

first: Feng

last: Guoqing


title: Loss of arginine methylation in Saccharomyces cerevisiae leads to the dysregulation of phosphate-associated genes and processes

city: Sydney

first: Chi Nam Ignatius

last: Pang

state: NSW

address: School of Biotechnology and Biomolecular Sciences, UNSW Australia

department: The NSW Systems Biology Initiative

institute: The University of New South Wales

summary: Hmt1p is the predominant arginine methyltransferase in Saccharomyces cerevisiae. Its substrate proteins are involved in transcription, transcriptional regulation, nucleocytoplasmic transport and RNA splicing. Functionally, Hmt1p-catalysed methylation can also modulate protein-protein interactions. Despite Hmt1p being well-characterised, the effects of its knockout on the proteome and transcriptome have not been reported. SILAC-based analyses of the hmt1Δ proteome, in mid-log exponential growth, revealed a decreased abundance of phosphate-associated proteins including Pho84p (phosphate transporter), Pho8p (vacuolar alkaline phosphatase), Pho3p (acid phosphatase) along with Vtc1p, Vtc3p and Vtc4p (subunits of the vacuolar transporter chaperone complex). RNA-Seq and microarray analysis revealed a downregulation of phosphate-responsive genes in hmt1Δ, including PHO5, PHO11 and PHO12 (acid phosphatases), PHO84 and PHO89 (phosphate transporters) and VTC3 (vacuolar transporter chaperone). Consistent with these observations, we observed a dysregulation of phosphate homeostasis in hmt1Δ, with a general decrease in extracellular phosphatase production and a decrease in total Pi in phosphate replete medium. We show that the transcription factor Pho4p, responsible for activation of the PHO pathway, can be methylated by Hmt1p at Arg-241 and is the likely cause of phosphate dysregulation in hmt1Δ. However, the methylation of Pho4p does not affect its nucleocytoplasmic localisation. We propose that the methylation of Pho4p may affect either its capacity to multimerise, its capacity to interact with Pho2p or target DNA, or may affect Pho4p phosphorylation at Ser-242 and/or Ser 243. Our study highlights a previously unknown function of Hmt1p in the regulation of phosphate homeostasis and suggests a means by which sensing of AdoMet may affect intracellular phosphate concentration.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Four wild-type Saccharomyces cerevisiae biological replicates versus three hmt1Δ biological replicates

first: Samantha

middle: Z

last: Chia

first: Yu-Wen

last: Lai

first: Daniel

last: Yagoub

first: Sophie

last: Lev

first: Chi

first: Zhiliang

first: Julianne

last: Djordjevic

first: Melissa

last: Erce

first: Gene

last: Hart-Smith

first: Marc

last: Wilkins


title: Circulating adipose fatty acid binding protein promotes obesity associated breast cancer development

city: Louisville

first: Bing

last: Li

state: Kentucky

address: 505 S Hancock St

department: Microbiology and Immunology

institute: University of Louisville

summary: It is still unclear that how obesity increases the risk of breast cancer. To address this question, we used mRNA microarrays to characterize mouse breast tumor EO771 cells treated with mouse recombinant A-FABP protein and compared the data from their controls.

overall_design: EO771 cells were seperated into A-FABP treated group (A-FABP+) and non A-FABP treated group (A-FABP-). They were treated with 100ng/ml recombinant mouse A-FABP and control PBS. Each condition was performed in duplicates.

first: Jiaqing

last: Hao


title: IL-17RA-signaling modulates CD8+ T cell survival, differentiation and exhaustion during Trypanosoma cruzi infection

city: Paris

first: Wilfrid

last: Richer

address: 26 rue d'Ulm

institute: Institut Curie

summary: We used microarrays to compare gene expression profile of spleen CD8 T cells from IL-17RA KO and WT mice at different time-point after T. cruzi infection.

overall_design: 9 WT mouse samples (3 samples at day 0 post infection -pi-, 3 samples at day 14pi and 3 samples at day 22pi); 9 IL-17RA KO mouse samples(3 samples at day 0 pi, 3 samples at day 14pi and 3 samples at day 22pi).

first: Jimena

last: Tosello

first: Eva

last: Acosta Rodriguez

first: Eliane

last: Piaggio


title: Identification of differentially expressed genes in benign and malignant mammary gland tumors of dog and their role in cancers of mammary gland

city: bareilyy

first: Shahid

last: Hussain

address: IVRI campus,Izzatnagar

department: Department of Veterinary Biotechnology

country: India

institute: ICAR-IVRI

summary: Using microarray technology, we aim to identify genes affecting the biology of mammary tumor cancers in dogs. Canine mammary gland tumors (CMGTs) are the most common neoplasms in sexually intact female dogs. CMGTs have been suggested as a model for studying human breast cancer because of several similarities, including the relative age of onset, risk factors, incidence, histological and molecular features, biological behavior, metastatic pattern, and responses to therapy.

overall_design: Nine surgically resected tumors were collected and used in experimental analysis with respect to two healthy mammary glands. All samples were used in duplicates.

first: Sajad

middle: A

last: Wani

first: Raj

middle: K

last: James Singh

first: Sonal

last: Saxena

first: Sameer

last: Shrivastava

first: A

last: Sharma

first: Ashok

last: Tiwari

first: Ravi

last: Gandham

first: Bishnu

middle: P

last: Mishra

first: Rajkumar

last: Singh


title: Impact of DNA demethylation agents (5-azacytidine or vitamin C) on gene expression in glioblastoma HSR-GBM1 cells

first: Justin

last: St. John

summary: Glioblastoma HSR-GBM1 cells have low mitochondrial DNA copy numbers which is associated with the abnormal DNA methylation patterns. By inducing DNA demthylation using 5azacytidine and vitamin C, HSR-GBM1 cells modulate their mitochondrial copy number and capability of differentiation.

overall_design: HSR-GBM1 cell line with three conditions: untreated control group, treated with 5 azacitidine and treated with vitamin C.  3 biological replicates of each condition.

first: Xin

last: Sun


title: Transcriptional signature in liver reveal seasonal metabolic adaptation in the night-migratory blackheaded buntings

city: Irvine

first: Vivek

last: Swarup

state: CALIFORNIA

address: 3400 Bio Sci 3

department: Neurobiology and Behavior

institute: University of California Irvine

summary: Purpose: Next-generation sequencing (NGS) has provided an opportunity to understand the underline processes invloved in migratory behavior. The goals of this study are to compare NGS-derived liver transcriptome profiling (RNA-seq) under migratory and non-migratory processes and understand the processes contributign under the physiological state.

overall_design: In total, 12 liver samples (6 x 2; one sample from each of the six time-points of both M and nM states) were sequenced and mapped against zebra finch genome. A range of 20-30 million 100 base single-end reads were generated for each liver sample

first: Devraj

first: Hiep

last: Le

first: Vinod

last: Kumar


title: Primate fetal hepatic response to maternal obesity: epigenetic signaling pathways and lipid accumulation

first: Sobha

last: Puppala

department: Genetics

institute: Texas Biomedical Research Institute

platform_organism:
Papio hamadryas
Homo sapiens


title: Induced DNA demethylation, genome instability and transcription


title: Cancer/testis Antigen-Plac1 Promotes Invasion and Metastasis of Breast Cancer

status: Public on Dec 25 2018

city: nanjing

first: li

last: yongfei

address: 140 hanzhong RD.

institute: nanjing medical unversity

summary:
PLAC1, cancer-testis antigen, is a crucial element in tumorigenesis and development programs for many cancers.
Overexpression of PLAC1 promoted invasion and metastasis of breast cancer cells in vitro and in vivo. Co-immunoprecipitation and immunofluorescence cell staining assays be used revealed that PLAC1 physically interact with Furin to degrade Notch1 and generate NICD (Notch1 intracellar domain) and further inhibit Pten, which is also supported by the microarray analysis.

overall_design:
Examination of gene expression pattern in 2 cell types.
----------------------------
KangChen Bio-tech


title: SCL establishes a global repressive environment and cooperates with Polycomb RYBP-PRC1 to suppress alternative lineages in blood-fated cells [ETO2 ChIP-seq]

first: Hedia

last: Chagraoui

overall_design: ETO2 Chip sequencing was performed from two independent wild type ES cell differentiation where we isolated at day 3.5 of EB formation FLK1+ mesodermal cells.

first: Catherine

last: Porcher


title: Impact of DNA demethylation agents (5-azacitidine or vitamin C) on DNA copy number in gliobalstoma HSR-GBM1 cells

summary: Glioblastoma HSR-GBM1 cells have low mitochondrial DNA copy numbers which is associated with the abnormal DNA methylation patterns. By inducing DNA demthylation using 5azacitidine and vitamin C, HSR-GBM1 cells modulate their mitochondrial copy number and capability of diffrentiation.

last: St John

first: Melinda

last: Ziino


title: AP4 regulates stem and Paneth cell homeostasis and promotes adenoma initiation in the intestine (small intestinal organoid)

city: Munich

first: Markus

last: Kaller

address: Thalkirchner Strasse 36

department: Institute of Pathology

institute: Ludwig-Maximilians-University Munich

summary: AP4 is frequently expressed in primary CRCs. However, the in vivo relevance of AP4 for development of intestinal tumor formation has not been analyzed by genetic approaches. ApcMin/+ mice with deletion of AP4 were generated and analyzed. The mRNA expression profiles of intestinal adenomas with and without functional AP4 were compared.

overall_design: AP4 deficient ApcMin/+ mice and wild-type ApcMin/+ mice were sacrificed at 16 weeks of age. 3 tumor RNA samples were obtained for each genotype; each tumor RNA sample represented a pool of 5 tumors isolated from the same mouse.

first: S

last: Jaeckel

first: M

first: Heiko

last: Hermeking


title: AP4 regulates stem and Paneth cell homeostasis and promotes adenoma initiation in the intestine (adenoma)


title: Homo sapiens whole blood infected with Candida spp. (here: Candida glabrata)

first: Philipp

last: Kämmer

summary: Homo sapiens fresh whole blood was infected with Candida glabrata. RNA-pool of both species extracted at 0min (control), 15, 30, 60, 120, 240 min. Samples are rRNA depleted. Measurement of Candida glabrata gene expression.

sample_organism:
Nakaseomyces glabratus
Homo sapiens

platform_organism:
Nakaseomyces glabratus
Homo sapiens

first: Sylvie

last: McNamara

first: Sascha

last: Brunke

first: Jörg

last: Linde


title: Transcriptome dynamics during adventitious root formation in cuttings of Cryptomeria japonica D.Don

city: Hitachi

first: Yuki

last: Fukuda

state: Ibaraki

department: Breeding Department, Breeding Division

institute: Forestry and Forest Products Research Institute, Forest Tree Breeding Center

summary: To reveal transcriptome dynamics during adventitious root formation in a coniferous tree, C. japonica, we conducted custom microarry experiments. Three parts from cuttings of easy-to-root clone of C. japonica were collected at eight time points during adventitious root formation. The results revealed major turning points on transcriptome toward adventitious root formation and the expression behavior of genes related to carbohydrate, plant hormone and others suggested the important biological changes for adventitious root formation.

overall_design: Base of cuttings (underground), middle of cuttings (above ground) and shoots including needles were collected at 8 time points (0 hpe (hour post excision), 0 hpi (hour post insertion, about 2 hpe), 3 hpi, 1 dpi (day post insertion), 3 dpi, 1 wpi (week post insertion), 3 wpi and 6 wpi). At each time point, samples were collected from three cuttings as biological replicates.

first: Tomonori

last: Hirao

first: Kentaro

last: Mishima

first: Mineko

last: Ohira

first: Yuichiro

last: Hiraoka

first: Makoto

last: Takahashi

first: Atsushi

last: Watanabe


title: Comparison of sRNA populations obtained using HD adapters in A thaliana, with NEB RecJ exonuclease or Superscript II enzymes

status: Public on Dec 20 2018

city: Norwich

first: Tamas

last: Dalmay

address: Earlham Road

department: School of Biological Sciences

institute: University of East Anglia

summary: Multiple companies produce RecJ exonuclease and RNA dependent DNA polymerase for making cDNA. Our standard protocol was developed based on the enzymes from Epicenter (epicenter was recently bought by the Illumina company). As an alternative for the enzymes from EPicenter, we tested the RecJ exonuclease from NEB and Superperscript II from Invitrogen in sRNA library construction using HD adapters [Sorefan et al 2012, Xu et al 2015].

overall_design: Construction of sRNA libraries using HD adapters using alternative enzymes (NEB RecJ exonuclease and Superscript II).

first: Martina

last: Billmeier

first: Irina

last: Mohorianu

first: Ping

last: Xu


title: Homo sapiens whole blood infected with Candida spp.

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

sample_organism:
Candida albicans
Nakaseomyces glabratus
Candida parapsilosis
Candida tropicalis
Homo sapiens

overall_design: Refer to individual Series


title: MiRNA expression in embryonic murine hepatocytes versus murine cholangiocytes at E18.5

city: Brussels

first: Claude

last: Gérard

address: Avenue Hippocrate 75

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

summary:
Differentially expressed miRNAs between hepatocytes (GFP-neg in SOX9-GFP mice) and cholangiocytes (GFP-pos in SOX9-GFP mice) in mice at E18.5.
We want to compare miRNA population in biliary cells and parenchymal cells (depleted from hematopoietic cells) during liver development. Cholangiocytes specifically express the transcription factor Sox9. This enables to separate cholangiocytes from the rest of the liver parenchyma by FACS from Sox9-GFP transgenic mice. In conclusion, we want to compare miRNA population in our GFP+ cells (cholangiocytes) and our GFP- cells (liver parenchyma depleted from hematopoietic cells).

overall_design: 200 ng of RNA were labelled and hybridized to miRCURY LNA array (7th Gen) by Exiqon S/A Profiling Services. Three biological samples, each representing a pool of 20 livers, of Sox9-GFP+ and Sox9-GFP- cells labelled with Hy3 or Hy5 were compared. miRNAs with Benjamini-Hochberg adjusted p-values < 0.05 were selected.

first: Frédéric

last: Lemaigre


title: Suppressor of cytokine signaling 1 is involved in gene regulation which control the survival of Ly6Clow monocytes in mice

status: Public on Dec 23 2018

city: Mainz

first: Frank

last: Rühle

address: Ackermannweg 4

department: Bioinformatics Core Facility

institute: Institute of Molecular Biology (IMB)

summary: Objective: Monocytes are crucially involved in inflammatory processes. In mice, different subsets of monocytes can be distinguished by the expression of Ly6C, a surface marker that is highly expressed on inflammatory monocytes (Ly6C high) and to a lesser extent on patrolling monocytes (Ly6C low). Our previous study revealed an aggravated accumulation of inflammatory Ly6C high monocytes in atherosclerotic-prone mice bearing a deficiency in suppressor of cytokine signaling (Socs)-1. In the present study, we performed a genome-wide analysis of Socs-1-dependent gene regulation in Ly6C high and Ly6C low monocytes.  Methods and Results: Monocyte subsets were isolated from socs-1+/+ rag2‒/‒ ldlr–/‒ and socs-1‒/‒ rag2‒/‒ ldlr-‒/‒ mice with subsequent identification of differential regulated genes using illumina MouseWG-6 v2.0 Expression BeadChip microarrays (45,200 transcripts). Principal component analysis illustrates a distinct separation of gene expression profiles in Ly6C high and especially Ly6C low monocytes from Socs-1 deficient mice. Additionally, microarray data revealed 46 genes to be differentially regulated in a Socs-1 dependent manner in both monocytic subsets by 2-fold or more, some of which were validated by qPCR (p<0.05, n=4-6). Among them, two principal regulators of monocyte differentiation, C-X3-C chemokine receptor 1 (Cx3cr1) and colony stimulating factor 1 receptor (Csf1r), were identified to be Socs-1 dependently regulated. Especially for Csf1r a co-expression network for correlating Socs-1 dependent gene expression and protein interaction could be compiled. Furthermore, in silico analysis of a transcription factor (TF) network correlating with Socs-1 dependent mRNA expression data revealed a cluster of TF that includes Nr4a1 as well as several ets-domain proteins that may interact and thus regulate gene expression, inter alia regression of Csf1r.   Conclusion: By genome-wide analysis, we could identify Cx3cr1 and Csf1r as two essential receptors mediating monocyte differentiation that are subjected to Socs-1 dependent transcription factor regulation.

overall_design: Total RNA obtained from Ly6C high and Ly6C low monocytes isolated from bone marrow of atheroprone mice with 3 different genotypes (SRL-/-: Socs1-/- Rag2-/- Ldlr-/- ;  RL-/-: Rag2-/- Ldlr-/-; L-/-: Ldlr-/-).

first: Jutta

last: Schütt

first: Julian

last: Kreutz

first: Karsten

last: Grote

first: Ann-Kathrin

last: Koch

first: Harald

first: Raghav

last: Oberoi

first: Anika

last: Witten

first: Monika

last: Stoll

first: Bernhard

last: Schieffer


title: Expression data in Esherichia coli wild type and ∆dnaK

city: Tokyo

first: Shinya

last: Sugimoto

address: 3-25-8 Nishi-Shimbashi

department: Department of Bacteriology

institute: The Jikei University School of Medicine

summary: We found that nemerous genes were up- or down regulated in ∆dnaK, including RpoS-regulated genes.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: To compare gene expression profile, E. coli strains were grown at 30C for 48 h in YESCA medium under static conditions for RNA extraction and hybridization on Agilent microarrays.

first: Ken-ichi

last: Arita-Morioka


title: Transcriptomic and epigenomic analysis during conversion from mouse microglia into induced-neuronal (iN) cells

status: Public on Dec 21 2018

city: Ikoma

first: Taito

last: Matsuda

institute: Nara Institute of Science and Technology

summary: Purpose: The goals of this study are to investigate the mechanisms underlying NeuroD1 (ND1)-mediated reprogramming.

overall_design: Methods: Transcriptomic and epigenomic profiles of control and ND1-transduced microglia at 2 day and 7 days post Dox treatment were generated by deep sequencing, using Illumina Hiseq 2500.

first: T

first: K

last: Nakashima


title: Gene-level differential expression analysis in hepatoblasts with or without mmu-miR-337-3p overexpression

first: Claude

summary:
Impact of mmu-miR-337-3p on the global gene expression in murine hepatoblasts.
We used microarrays to identify the genes controlled by mmu-miR-337-3p in in vitro cultured hepatoblasts. We identified distinct classes of up-regulated / down-regulated genes.

overall_design: In vitro cultures of immortalized hepatoblasts (BMEL) from E12.5 wild-type mice liver were transfected with microRNA mmu-miR-337-3p mimic or microRNA mimic negative control. 3 replicates each.


title: Functional changes of AMPA responses in human induced pluripotent stem cell-derived neural progenitors in fragile X syndrome

status: Public on Dec 19 2018

city: Helsinki

first: Maija

middle: L

last: Castrén

state: Helsinki

address: P.O.BOX 63

department: Faculty of Medicine/Physiology

country: Finland

institute: University of Helsinki

summary: Transcriptome analysis of RNA samples collected from human control and FXS iPS cell-derived neural progenitors at day 1 of differentiation.

overall_design: In this study, we analyzed gene expression profile of human iPS cell-derived neural progenitors reprogrammed from somatic cells of 3 healthy subjects and 3 patients diagnosed with FXS using the Affymetrix ClariomTM D Human array. No technical replicates were performed.

first: V

middle: S

last: Achuta

first: Tommi

last: Möykkynen

first: Ulla-Kaisa

last: Peteri

first: Giorgio

last: Turconi

first: Claudio

last: Rivera

first: Kari

last: Keinänen


title: H3K27 tri-methyltransferases CLF and SWN redundantly buffer ABA-induced senescence

status: Public on Dec 14 2018

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

summary: The phytohormone abscisic acid (ABA) induces senescence and facilitates nutrient reuse, which are essential for increasing stress tolerance. Senescence controls plant aging and is closely associated with crop yield and quality. It is a complicated process finely tuned by multiple layers of control. A significant proportion of ABA-responsive genes and cis-elements are targeted by H3K27me3 modification that is mediated by Polycomb group proteins (PcGs); however, the interplay between the major epigenetic machinery and the central stress hormone is poorly understood. Both pathways influence the transcription of thousands of genes, and the dynamic and quantitative epigenomic and transcriptomic changes cannot be characterized with high confidence. This issue is further complicated by the redundant roles of PcG components. This article revealed an intriguing mechanism of the interplay between ABA and PcG in regulating plant senescence, based on the integration of genetic evidence and quantitative comparison of epigenomic data derived from a purpose-developed computational model. We observed that >30% of ABA-induced genes are up-regulated in a double mutant of H3K27me3 methyltransferases CLF and SWN; and the double mutant, but not single-gene mutants, is hyper-sensitive to ABA treatment. Importantly, ABA-triggered H3K27me3 reduction preferentially occurred in regions around senescence-associated genes (SAGs), which are redundantly repressed by CLF and SWN in normal conditions. Furthermore, we revealed that the presence of H3K27me3 surrounding SAGs does not block ABA-induced SAG expression, but rather limits the extent of the induction, thereby preventing an over-sensitive response within a dynamic environment. These findings may serve as a paradigm for the crosstalk between the rapid-effect of phytohormone and the long-term effect of epigenetic machinery in regulating plant environmental responses through modulations of the senescence process.

overall_design: Arabidopsis thaliana seedlings were grown on 1/2 Murashige and Skoog (MS) medium without sucrose (2% agar, PH 5.8) under LDs conditions. clf-50swn-1 is in the Ws background. For ABA treatment, 10-d old seedlings were transferred onto 1/2 MS medium containing 50 uM ABA or 100 uM ABA. After 4 days' treatment, the aerial parts were harvested, either frozen in liquid nitrogen for RNA isolation or directly vacuum-infiltrated with formaldehyde crosslinking solution for ChIP assay.

first: Yijing

last: Zhang


title: Global transcriptional control by the transcriptional regulator SinR in Clostridium difficile

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

institute: Institut Pasteur

overall_design: Two-conditions experiments, 630E strain vs SinR mutant grown in TY 7h, 4 biological replicates for each condition

first: Laure

last: Saujet


title: Regulation of Pol II pausing is involved in daily transcription in the mouse livers in the mouse liver

city: Wuhan

first: Xiaodong

last: Li

state: Hubei Province

address: Luojia Hill, Wuchang District

department: College of Life Sciences

institute: Wuhan University

summary:
Purpose: We used ChIP-seq to analyze daily transcription and regulation of Pol II pausing within the mouse liver.

Methods:  Livers of young mice were processed for Pol II and Nelf-A ChIP-seq at 4-h interval across the day. The binding pattern was analyzed by MACS. Tag pileup within promoter and gene body regions were also obtained to calculate Pol II TR.

Results: We obtained > 10 million high quality sequencing reads per time points per sample after quality control and alignments. MACS identified nearly 10,000 Pol II peaks genomewide throughout the day. Nelf-A peaks varied from a few hundreds to 10,000 across the day. A genomewide Nelf-A binding rhythm was evident. We also quantitated bindings within the TSS region and/or gene body and analyzed the quantitation results with ARSER for rhythm detection. We found Pol II binding within the TSS region and gene body show discordant changes.  While most genes had peak TSS Pol II binding around dawn, Pol II binding within the gene body showed more scattered distribution, with two peaks around dawn and dusk, respectively. Pol II traveling ratio also showed daily changes, with most genes having a higher TR around dawn.

Conclusions: Our study revealed discordant Pol II rhythms in the TSS region and within the gene body, and indicated that Pol II initiation and pause release could have distinct roles in the generation of transcription rhythms within the mouse liver.

overall_design: Mouse liver chromatin was prepared at 4-h interval across the day and used in ChIP-seq with Pol II, Nelf-A and Tbp antibodies.

first: Chengwei

first: Jialou

last: Zhu

first: Changxia

last: Gong

first: Jianguo

last: Wu


title: The effect of aging and high fat diet on gut microbiota in aged F344 rats

status: Public on Dec 18 2018

city: Seongnam-si

first: Nayoung

last: Kim

state: Gyeonggi-do

address: 82 Gumi-ro, 173 Beon-gil, Bundang-gu

department: Department of Internal Medicine

institute: Seoul National University Bundang Hospital

summary: This study was performed to investigate the effect of aging and high fat diet on gut microbiota in F344 rats by the pyrosequencing method.

overall_design: Metagenome analysis was performed on microbiota from stools of 6-week old and 2-year old rats fed with chow or high fat diet. There were 8 groups: 6-week old male control (n = 6), 6-week old male high fat diet (n = 6), 6-week old female control (n = 6), 6-week old female high fat diet (n = 6), 2-year old male control (n = 4), 2-year old male high fat diet (n = 4), 2-year old female control (n = 5), and 2-year old female high fat diet (n = 5).

first: SunMin

last: Lee

first: JiHyun

last: Park

first: RyoungHee

last: Nam

first: Daeun

last: Choi

first: Yeong-Jae

last: Seok

first: Yeon-Ran

first: Hyuk

last: Yoon

first: Sung-Hwa

last: Sohn

first: JungMin

first: DongHo


title: Mechanisms of Cancer Resistance to Immunogenic Cytotoxicity

city: Houston

first: Yu

middle: Leo

last: Lei

address: 1901 East Rd

department: Head and Neck Surgery

country: USA

institute: The University of Texas M.D. Anderson Cancer Center

summary: The majority of cancer patients do not respond to immunotherapy. In order to systematically discover pathways promoting cancer cell resistance to effector immune cells, we generated immunity-resistant Head and Neck Squamous Cell Carcinoma cell lines. We utilized RNA-Seq to determine what are the genes and pathways that are significantly altered when cancer cells become resistant to effectors.

overall_design: RNA-Seq was performed on four cell lines, including two biologic replicates of wildtype and immune-resistant PCI-13 cells. The two immune-resistant PCI-13 cell lines were generated separately using the same protocol described in the manuscript.

first: Yuying

last: Xie