first: Yasuhiro

last: Yamada

summary: Clear cell sarcoma (CCS) is a rare soft tissue sarcoma caused by the EWS/ATF1 fusion gene. Here, we established induced pluripotent stem cells (iPSCs) from EWS/ATF1-controllable murine CCS cells harboring sarcoma-associated genetic abnormalities. Sarcoma-iPSC mice develop secondary sarcomas immediately after EWS/ATF1 induction, but only in soft tissue. EWS/ATF1 expression induces oncogene-induced senescence in most cell types in sarcoma-iPSC mice but prevents it in sarcoma cells. We identify Tppp3-expressing cells in peripheral nerves as a cell-of-origin for these sarcomas. We show cell type-specific recruitment of EWS/ATF1 to enhancer regions in CCS cells. Finally, epigenetic silencing at these enhancers induces senescence and inhibits CCS cell growth through altered EWS/ATF1 binding. Together, we propose that distinct responses to premature senescence are the basis for the cell type-specificity of cancer development.

overall_design: Microarray in mouse EWS/ATF1-induced sarcoma cell lines(G1297), G1297-derived iPSCs(sarcoma iPSC) and sarcoma iPSC-derived MEF(sarcoma MEF), and surgically resected human sarcoma samples (clear cell sarcoma; CCS and malignant peripheral nerve sheeth tumor; MPNST) and human clear cell sarcoma cell line with EWS/ATF1 knocked down. Total 26 samples (10 murine samples/16 human samples) were analized. In G1297 and its derivatives, we can induce EWS/ATF1 by Doxycycline-inducible expression system. We compared global gene expression change caused by EWS/ATF1 induction  between G1297 and sarcoma MEF. Also, we investigated global gene expression pattern of sarcoma iPSCs and surgically resected human CCS and MPNST. A link to this sample file can be found below.

first: Shingo

last: Komura

first: Fumiaki

last: Itakura


title: Dynamic gene network analysis of Caco-2 cell response to Shiga toxin-producing Escherichia coli-associated hemolytic-uremic syndrome

status: Public on Jul 15 2019

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

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

overall_design: Refer to individual Series


title: UPF1/SMG7-dependent MicroRNA-mediated Gene Regulation

status: Public on Jun 30 2019

city: Seoul

first: Jin-Wu

last: Nam

address: Seongdong-Gu Hangdang-dong

department: Department of Life Science

country: South Korea

institute: Hanyang University

type: Expression profiling by high throughput sequencing

summary: A majority of metazoan mRNAs are under microRNA (miRNA)/Argonaute (Ago)-mediated control of RNA stability at the post-transcriptional level. Although the molecular mechanism of the miRNA-mediated repression of target mRNAs through Ago/TNRC6 pathway have been largely elucidated, however, the existence of alternative TNRC6-independent miRNA-mediated post-transcriptional gene regulation pathway remains unknown. Here, we suggest that endogenous miRNAs (endo-miRNAs) can downregulate the target mRNAs via the alternative molecular pathway, Ago-associated UPF1/SMG7, core mediators of nonsense-mediated mRNA decay. Global analyses of mRNAs in a response to UPF1 RNA interference in miRNA-deficient cells reveal that 3’UTR-length-dependent mRNA decay by UPF1 requires endo-miRNA targeting via CUG motif. The repression of miRNA targets is more additively or synergistically accomplished by combination of Ago2 and UPF1 through UPF1-associated SMG7, recruiting CCR4-NOT deadenylase complex, in TNRC6-independent manner. We expect that the new miRNA-mediated mRNA decay pathway enables the miRNA targeting to become more predictable and expand the miRNA-mRNA regulatory network.

overall_design: Examination of 11 different knockdown condition in HeLa cell type

first: JW

last: Hwang

first: JY

last: Park

last: Seo


title: Perivascular macrophages proliferate in the CNS, but also contributed by bone-marrow precursors in response to cerebral ischemia

city: Warsaw

first: Bartosz

last: Wojtas

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

summary: Immune response following CNS disease and injury comprises three different compartments, parenchymal, perivascular and blood involving specialized immune cells. Microglia are the major immune cell residing in the CNS parenchymal compartment but together with other macrophages which are residing in the non-parenchymal structures such as perivascular spaces, leptomeninges and choroid plexus constitute the total macrophage population of the CNS. While the homeostatic functions of these specialized macrophages in not very well understood, evidence shows that these macrophages at the blood-brain interface might involve immune-surveillance and establish a gate way for the recruitment of peripheral immune cells in to the CNS in response to the pathological stimuli. In humans and rats these macrophages identified exclusively by the high levels of scavenger receptor CD163

overall_design: RNAseq profilling of CD11b+CD163+ sorted cells after MCAO compared to CD11b+CD163+ sham cells

first: Wenson

last: Karunakaran


title: The pathogenesis of diclofenac induced immunoallergic hepatitis in a canine model of liver injury

city: Hannover

first: Juergen

last: Borlak

state: Lower Saxony

address: Feodor-Lynen-Str. 35

department: Centre for Pharmacology and Toxicology

country: Germany

institute: Hannover Medical School

summary: Diclofenac is a non-steroidal anti-inflammatory drug (NSAID) commonly used for the treatment of arthritis and chronic pain associated with musculoskeletal injuries. However, its use is associated with a variety of adverse drug reaction, including rare but severe hepato- and nephrotoxicity. The molecular mechanism leading to diclofenac induced immunoallergic hepatitis is unknown. The objective of this study is to identify the molecular mechanisms involving immune mediated inflammatory reactions and its link to DILI through whole genome gene expression profiling.

overall_design: Beagle dogs were given 1 (LD, N=3) or 3 mg/kg/day (HD, N=3) oral diclofenac for 28 days. Control animals (N=3) received empty gelatine capsules. Clinical signs, serum biochemistry, blood smear and serum/urinary electrolytes were determined on day 1, 15 and 28. Histo- and immunopathology revealed causes of allergic hepatitis. The whole genome gene expression profiling of liver and kidney were examined to define the molecular mechanism of diclofenac induced immune mediated organ toxicity.

first: Saravanakumar

last: Selvaraj

first: Jung-Hwa

last: Oh

first: Reinhard

last: Spanel

first: Eun-Hee

last: Lee

first: Hyoung-Yun

last: Han

first: Seokjoo

last: Yoon

first: Jürgen


title: miRNAs expression in breast cancer tumor tissues with or without axillary lymph nodes metastastsis

city: guangzhou

first: xinhua

last: xie

state: guangdong

address: dongfeng east road

country: China

institute: Sun Yat-sen University Cancer Center

summary: Differential RNAs expression analysis by microarray was used to identify miRNAs differentially expressed in primary breast cancer tumor tissues that have developed axillary lymph nodes metastases or not. To generate miRNA expression profiles, 24 fresh tumour samples were obtained from breast cancer patients whose tumor size are less than 3cm at Sun Yat-sen University Cancer center.

overall_design: Twelve patients with axillary lymph node metastasis were matched with the other twelve patients who were axillary lymph noedes non-metastasis according to tumor size and molecular subtypes. We then assessed differential miRNAs expression between primary tumor tissues with or without lymph node metastasis pathologically.

first: Xinhua

last: Xie

first: Xiaoming


title: SETD5 is a H3K36 methyltransferase which preserves transcriptional fidelity during brain development and neuronal wiring [ChIP-seq]

status: Public on Jul 10 2019

city: Trento

first: CIBIO

last: Zippo

state: Not Applicable

address: via sommarive 9

department: Cellular, Computation and Integrative Biology (CIBIO)

country: Italy

institute: University of Trento

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We assess the epigenetic function of Setd5 in mouse neural stem cells (NSCs), by profiling a panel of histone modifications and Setd5 binding in wild type and Setd5 heterozygous NSCs.

overall_design: ChIP-seq for H3K4me3, H3K4me1, H3K27ac, H3K27me3, H3K36me2, H3K36me3 in wild type and Setd5+/- NSCs and ChIP-seq for SETD5-V5 in wild type NSCs.

first: Luca

last: Fagnocchi

first: Alessio


title: Photoactivatable-Ribonucleotide-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) of RNA-binding proteins (RBPs), LIN28A, LIN28B Igf2bp3 and Pum2 in 220-8 mouse cell lines

status: Public on Jun 27 2019

city: Bethesda

first: Stefan

middle: A

last: Muljo

state: MD

address: 10 CENTER DR RM 11N306

country: USA

institute: NIH/NIAID

summary: Transcriptome-wide profiling of RNA-binding by four RBPs in v-Abl transformed 220-8 pro-B mouse cell line. Binding sites are characterized by T-to-C cross-linking mutations, depth, location on transcript, and overlap/exclusivity across different RBPs.

overall_design: Four biological replicates of PAR-CLIP are provided each for LIN28A, LIN28B and Igf2bp3. One replicate provided for Pum2.

first: Markus

last: Hafner


title: The RNA-binding proteins Igf2bp3 and Lin28b cooperate to control a fetal-adult hematopoietic switch


title: Cell-type dependent enhancer binding of the EWS/ATF1 fusion gene in clear cell sarcomas

status: Public on Jul 18 2019

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

country: Japan

institute: University of Tokyo

overall_design: ChIP-seq was performed with mouse EWS/ATF1-induced sarcoma cell line (G1297),  Ebf1- and Nanog-KRAB-introduced G1297 and sarcoma iPSC-derived MEF(sarcoma MEF). Total 9 samples (5 ChIP/ 4 input) were analized. In G1297 and its derivatives, we can induce EWS/ATF1 by Doxycycline (Dox)-inducible expression system. We compared binding pattern of EWS/ATF1 after Dox treatment between G1297 and sarcoma MEF, Ebf1-KRAB-introduced-G1297 and Nanog-KRAB-introduced G1297.

first: Shingo

last: Komura

first: Fumiaki

last: Itakura


title: Low-input RNA-seq experiment to identify genes with a similar expression pattern to that of Lin28b

summary: Genome-wide profiling of RNA expression in two sub-populations of hematopoietic stem cells from mouse Fetal Liver (FL) and adult Bone Marrow (BM)

overall_design: Expression profiles generated for common lymphoid progenitor (CLP) cells and lineage-negative Sca1-positive kit-positive (LSK) cells in FL and BM.


title: RNA-seq experiment to identify differentially expressed genes due to the transduction of LIN28A

summary: Genome-wide profiling of RNA differential expression in v-Abl transformed 220-8 pro-B mouse cell line

overall_design: Expression profiles generated for 220-8 cell lines with and without hLIN28A retroviral transduction


title: Competing endogenous RNA expression dataset from placenta tissues of normal human and  patients with severe preeclampsia.

city: shanghai

first: xiaopeng

last: hu

address: dongchuan road 800

institute: shanghai jiaotong university

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

summary: We used microarray to detail Competing endogenous RNA expreession  in placenta tissues from normal human and patients with severe preeclampsia

overall_design: placenta tissues from normal human and patients with severe preeclampsia were for RNA extraction and hybridization on  Agligent microarrays

first: ji

last: wu

first: weiwei

last: cheng


title: CircRNA expression profiles in early stage lung adenocarcinoma

status: Public on Jun 26 2019

city: Shanghai

first: Ming

last: Xu

address: 280 Mohe Road

department: Oncology

institute: Shanghai 9th People's Hospital, Shanghai Jiao Tong University School of Medicine

summary:
To determine the circRNA expression profile in early stage lung adenocarcinoma and matched non-tumor tissues, we used circRNA microArray analysis form Arraystar to examine the expression of circRNAs
Lung adenocarcinoma, a form of NSCLC with high lethality at advanced stage, is becoming more popular in women, non- or never-smokers, and even young adult. However, there are no effective early diagnosis methods at present for patients to cure timely. Circular RNAs (circRNAs) as a special novel, stable, and conserved non-coding RNA in mammalian cells have been reported to be widely involved in the processes of cancer disease. Yet, it is still a puzzle which specific circRNAs are involved in the development of early stage lung adenocarcinoma. Here, tumour samples and paired adjacent normal tissues from 4 patients with early stage lung adenocarcinoma were selected for investigating the expression profile of circRNAs by using the high-throughput circRNA microarray. Bioinformatic analyses were conducted to screen those differentially expressed circRNAs. This work illustrates that clusters of circRNAs are aberrantly expressed in early stage lung adenocarcinoma, which might be able to provide potential targets for the early diagnosis of this disease and new genetic insights into lung cancer.

overall_design: Early stage lung adenocarcinoma tissues from surgery were distributed into two experimental groups: tumor tissue group and adjacent normal tissue group, then perform circRNAs chips by Arraystar Human circRNAs chip (Arraystar)

first: Jiangmin

last: Zhao

first: Bin

last: Jiang

first: Le

last: Li

first: Haihua

last: Yuan

first: Hongxiu


title: Trunk events present minimal intra- and inter-tumoral heterogeneity in hepatocellular carcinoma [multinodular CNV]

status: Public on Jul 05 2019

city: Barcelona

first: Sara

last: Torrecilla

state: Catalonia

address: Rossello Street, 149

country: Spain

institute: IDIBAPS

summary: Introduction: According to the clonal model of tumor evolution, trunk alterations arise at early stages and are ubiquitous. Through the characterization of early stages of hepatocarcinogenesis, we aimed to identify trunk alterations in HCC and study their intra- and inter-tumor distribution in more advanced lesions.    Methods: 151 samples representing the multi-step process of hepatocarcinogenesis were analyzed by targeted-sequencing and SNP array. Genes altered in early lesions [31 dysplastic nodules (DNs) and 38 small HCCs (sHCC)] were defined as trunk. The distribution of candidate trunk genes was explored in: a) different regions of large tumors [43 regions of 21 tumors, (2-3 regions/tumor)]; and b) different nodules of the same patient [39 multinodular tumors from 17 patients]. Multinodular lesions were classified as intrahepatic metastases (IMs) or synchronous tumors based on chromosomal aberrations.     Results: TERT promoter mutations (10.5%) and broad copy-number aberrations in chromosomes 1 and 8 (3-7%) were identified as trunk gatekeepers in DNs and were maintained in sHCCs. Trunk drivers identified in sHCCs included TP53 (23%) and CTNNB1 (11%) mutations, and focal amplifications or deletions in known drivers (6%). Overall, TERT, TP53 and CTNNB1 mutations were the most frequent trunk events in early stages. 89% of mutations in these genes were shared between different regions of large tumors. In multinodular HCCs, 35% of patients harbored IMs. 85% of mutations in TERT, TP53 and/or CTNNB1 were retained in primary and metastatic tumors.    Conclusions: Trunk events in early stages (TERT, TP53, CTNNB1 mutations) were ubiquitous across different regions of the same tumor and between primary and metastatic nodules in >85% of cases. This concept supports the knowledge that single biopsies would suffice to capture trunk mutations in HCC.

overall_design: 39 paraffin-embedded tumors from 17 patients presenting multinodular cases (2-3 nodules/patient) were collected and gDNA was extracted. Matched non-tumor cirrrhotic tissue was also collected for all cases. Comparative Genomic Hybridization analysis was done using HumanOmniExpress-12v1 BeadChip (Illumina) according to manufacturer’s protocols. Previous treatment with the Infinium FFPE restoration kit (Illumina) was performed. Log R ratio (LRR, reflecting total copy number) and B-allele frequency (BAF) obtained from GenomeStudio were used for CNV detection.

first: Josep

middle: M

last: Llovet

first: Zhongyang

last: Zhang

first: Ke

last: Hao


title: Identification of the coiled-coil domain as an essential element of MBD3 for preserving lineage commitment potential of ESCs

status: Public on Jun 25 2019

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Research Center for Genomic Medicine

institute: Saitama Medical University

summary: We explored the effect of knockout of Mbd3 gene on global expression profile in ESCs and compared the ability to counteract such alteration among three isoforms of MBD3, i.e. MBD3a, b and c.

overall_design: ESCs that are completely null for MBD3 (Mbd3abc-KO ESCs) were generated using EBRTcH3 ESCs as wild-type ESCs. Expression vectors for either MBD3a, b or c or one of deletion mutants of MBD3a in MBD and/or coiled-coil domains were stably introduced into Mbd3abc-KO ESCs and then such Mbd3abc-KO ESCs bearing one of transgenes were cultured with or without LIF for 12 days. Mbd3abc-KO ESCs bearing the empty vector was also generated as a control.

first: Masataka

last: Hirasaki

first: Yutaka

last: Nakachi

first: Yosuke

last: Mizuno

first: Yasushi

last: Okazaki


title: miRNAs expression in swine monocytes stimulated with Bifidobacterium animalis ssp. lactis Bb12

city: Hermosillo

first: Marina

last: Arenas-Padilla

state: Sonora

address: Carretera Gustavo Enrique Astiazarán Rosas 46

country: Mexico

institute: Centro de Investigación en Alimentación y Desarrollo A. C.

summary: Bifidobacterium animalis ssp. lactis Bb12 (Bb12) is a probiotic bacteria with several reported benefits, including immunomodulatory capacity. This is due to the bacteria recognition by receptors such as TLR2, which in turn affects the miRNA transcriptome of immune system cells. We aimed to analyze miRNA expression in swine monocytes stimulated with Bb12, and their expression when TLR2 receptor is blocked. A microarray containing 407 porcine unique miRNA probes was employed to identify differences in the miRNA expression pattern in swine monocytes in response to Bb12. A total of 143 were differentially expressed miRNAs (p<0.05); out of which, 87 miRNAs are statistically significant but have lower signals (signal <500).

overall_design: Swine monocytes from peripheral blood were stimulated with Bifidobacterium animalis ssp. lactis Bb12 for 4 hours, with and without anti-TLR2 blocking antibody. Biological replicates: 1; Array replicates: 8.

first: Veronica

last: Mata-Haro


title: Colorectal Cancer-derived Small Extracellular Vesicles Create an Inflammatory Pre-metastatic Niche through Macrophage Polarization in Liver Metastasis

status: Public on Jul 01 2019

city: Hangzhou

first: yingkuan

last: Shao

address: Jiefang Road 88

institute: Zhejiang Universit

summary: Colon and liver have an inseparable relationship since embryological development. More than half of colorectal cancer patients developed liver metastases accompanied with poor prognosis. Recent evidence suggests that distant metastatic organs are “educated” by primary tumor-derived extracellular vesicles. Here we found that the liver-specific pro-metastatic effect of colorectal cancer (CRC)-derived small extracellular vesicles (sEVs). In vivo experiments showed that the injected fluorescence-labeled CRC-derived sEVs were accumulated and taken up by macrophages in the mouse liver. MicroRNA sequencing revealed the highest expression of microRNA (miR)-21-5p in CRC-derived sEVs. In vitro co-culture experiments showed that the sEVs polarized macrophages toward an interleukin-6(IL-6)-secreting type of macrophages. Further mouse experiments and microarray studies indicated that the CRC-sEVs increased macrophage invasion and induced an inflammatory microenvironment in the liver, which promoted liver metastasis of orthotropic- transplanted CRC cells. Most importantly, the TCGA data analysis and clinical sample examinations demonstrated that miR-21-5p expressions were sharply raised in the CRC tissues. We apply Tethered Cationic Lipoplex Nanoparticles (tCLN) technology in detecting CRC patients’ sEVs miR-21 in plasma and found strong correlation between sEVs-miR-21 and CRC liver metastasis. The serum IL-6 level was much higher in CRC patients with liver metastasis, and the liver metastasis relevance of MiR-21, macrophages, and IL-6 in CRC patients. Thus, we propose the role of CRC-derived sEVs in the formation of an inflammatory pre-metastatic niche in liver for CRC metastasis through macrophage polarization via a miR-21/TLRs pro-inflammation pathway.

overall_design: Purified SW620-derived sEVs were injected to nude mice via tail vein every other day for 21 days (each injection with 20 μg sEVs, totally 10 injections per mouse). The mice in the control group were injected with sterile PBS. Each group had 5 nude mice, all of which were alive normally before harvested, and there was no obvious weight difference between the experimental and control groups. Three nude mice were randomly picked from the experimental group, and after gas anesthesia, their livers were dissected and immediately stored in liquid nitrogen. Microarray screenings demonstrated that the expression of genes associated with inflammation, cell apoptosis, and excretal cellular matrix (ECM) remodeling was significantly altered.

first: Yingkuan

first: Ting

last: Chen


title: Changes in the plant host factors induced upon viral infection of Nicotiana benthamiana with peanut stunt virus (PSV)  [strain P] with and without satellite RNA

status: Public on Jun 22 2019

city: Poznan

first: Agnieszka

last: Zmienko

address: Noskowskiego 12/14

institute: Institute of Bioorganic Chemistry PAS

summary: Peanut stunt virus (PSV) belongs to cucumoviruses which infect many agriculturally important plants. Certain PSV strains contain a small RNA molecule, referred to as satellite RNA (satRNA), which has a propensity to modulate pathogenesis process.Plant viruses with ssRNA genomes are known to replicate in cytoplasm, however, they utilize other cellular structures to their life cycle as well. Among them the role of chloroplast is recently particularly underlined. Here, we tried to indicate the host factors associated with various cellular structures, the levels of which are changed during virus infection. To this end we did transcriptome profiling of N. benthamiana challenged by PSV-P with/ without satRNA using species-specific microarrays.

overall_design: Agilent microarrays in 2x105k format (two microarrays per slide) were used  for hybridization of labeled RNA from upper parts of treated N. benthamiana plants (infected PSV-P, PSV-P+satRNA) labeled with Cy5 versus a common reference (ref): pooled RNA extracted from a mix of tissues and treatments, labeled with Cy3. Three biological replicates were used for each treatment.

first: Michal

last: Goralski

first: Aleksandra

last: Obrepalska-Steplowska


title: Epigenetic profiling of enhancers in primary glioblastoma tissues

city: La Jolla

first: Leo

last: Kim

state: CA

address: 9500 Gilman Drive #0695

department: Medicine

institute: UC San Diego

summary: Glioblastomas are lethal cancers defined by inevitable disease recurrence after maximal surgical and chemoradiological interventions. To identify possible dependencies in glioblastomas undetected by whole transcriptome sequencing, we examined the enhancer landscape marked by histone 3 lysine 27 acetylation (H3K27ac) in primary glioblastoma specimens through ChIP-seq.

overall_design: ChIP-seq experiments on H3K27ac-enriched DNA elements from primary glioblastoma patient tissues

first: Xiuxing

last: Wang

first: Stephen

middle: C

last: Mack

first: Tyler

middle: E

last: Miller

middle: J

first: Jeremy

middle: N

last: Rich


title: Knockdown of CFIm25 or CFIm68 decreases RNA polymerase II pausing and transcription

status: Public on Jun 20 2019

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

summary: Transcription of eukaryotic protein-coding genes by RNA polymerase II (pol II) is highly regulated at initiation, elongation and termination and these steps are coordinated with co-transcriptional processing of the emerging pre-mRNA by capping, splicing, and cleavage and polyadenylation. Polyadenylation (Poly(A)) site recognition, which defines the end of the mRNA, relies on the cleavage and polyadenylation (CPA) complex. It was previously observed that knocking-down proteins of the CPA complex affects not only recognition of the poly(A) site but also results in increased pausing of pol II at the beginning of genes. This finding suggests that the CPA complex plays a role in regulating pol II turnover after transcription initiation. To explore this possibility, we knocked-down two subunits of the cleavage factor I (CFIm), CFIm25 and CFIm68, which are part of the CPA complex and involved in alternative polyadenylation, and performed pol II ChIP-seq. Surprisingly, we found that contrary to the effect of knocking down of other CPA factors, reduction of the level of CFIm25 or CFIm68 decreases pol II pausing and transcription genome-wide in HEK293 cells. These findings indicate that different subunits of the CPA complex have opposite effects on pol II pausing at the start of genes.

overall_design: Examination of the effect of CFIm68 knockdown on RNA polymerase II in HEK293 cells after 30 minutes treatment with DMSO or DRB.

first: Jessica

last: Hardy

first: Chris

last: Norbury

first: Shona

last: Murphy


title: Whole transcriptome sequencing of the human thyroid primary cells with knock-down of the NRG1 gene

status: Public on Jun 19 2019

city: Columbus

first: Yanqiang

state: Ohio

address: 12th w street

institute: The Ohio State University

summary: The protein encoded by the NRG1 gene is a membrane glycoprotein that mediates cell-cell signaling and plays a critical role in the growth and development of multiple organ systems. Here we report gene expression profiles of human thyroid primary cells on Day 5 treated with NRG1 siRNA. The primary cells were generated from fresh nontumorous thyroid tissues obtained from thyroid cancer patients. A number of new dysregulated genes of NRG1 were discovered. This study reveals a novel role of NRG1 in downstream gene regulation and provides a new explanation of NRG1’s function in thyroid cancer.

overall_design:
Profiling of 3 human thyroid primary cells (generated from 3 different patient samples) transfected with NRG1 siRNA (75pmol) was performed using RNA-seq. Cells were cultured for 24h after transfection and then lysed prior to RNA isolation, DNase treatment, purification and RNA-seq library construction.
Profiling of 3 human thyroid primary cultures (3 nontarget siRNA treated) derived from the fresh thyroid tissues of 3 individuals was also performed using RNA-seq.

first: Albert

last: de la Chapelle

first: Huiling

last: He


title: Functional properties of dietary protein sources towards the gut and systemic metabolism in pigs.

city: Wageningen

first: Dirkjan

last: Schokker

address: Droevendaalsesteeg 1

department: Wageningen Livestock Research

country: Netherlands

institute: Wageningen UR

summary:
This study was designed to address key questions concerning the use of alternative protein sources for animal feeds and addresses aspects such as their nutrient composition and impact on gut function.
The transcriptional response of intestinal mucosal tissue (jejunum and ileum) served as parameters for the local response. Growing pigs (BW 35 kg/approx. 10 weeks) were fed with experimental diets containing a single, common or new protein sources viz. soybean meal (SBM), black soldier fly larvae (BSF), spray dried blood plasma (SDPP), rapeseed meal (RSM), and wheat gluten meal (WGM) over a period of 4 weeks.

overall_design: Male pigs were stratified according to bodyweight and litter of origin into five dietary treatment groups. These pigs were fed for four weeks with semi-synthetic diets containing one of the following protein sources. At the end of four weeks, pigs were sacrificed by euthenesia and ileal tissue samples (scrapings) were collected for RNA extraction and hybridization on Agilent microarrays. Soybean meal (SBM) diet group served as reference to make comparisons with other experimental diets.

first: Soumya

middle: K

last: Kar


title: Metformin alters human host responses to Mycobacterium tuberculosis in-vitro and in healthy human subjects [Ex vivo Blood RNA-Seq]

status: Public on Jun 16 2019

city: London

first: Jackie

last: Cliff

address: Keppel Street

department: Immunology and Infection

institute: London School of Hygiene & Tropical Medicine

summary: Metformin, the most widely administered diabetes drug, has been proposed as a candidate for host directed therapy for tuberculosis although very little is known about its effects on human host responses to Mycobacterium tuberculosis. When added in vitro to PBMCs isolated from healthy non-diabetic volunteers, metformin increased glycolysis, inhibited the mTOR targets, strongly reduced M. tuberculosis induced production of TNF-α (-58%), IFN-gamma (-47%) and IL-1β (-20%), while increasing phagocytosis. In healthy subjects, in vivo metformin intake induced significant transcriptional changes in whole blood and isolated PBMCs, with substantial  down-regulation of genes related to inflammation and the type 1 interferon response.   Metformin intake also increased monocyte phagocytosis (by 1.5 to 2 fold) and ROS production (+20%). These results show that metformin in humans has a range of potentially beneficial effects on cellular metabolism, immune function and gene-transcriptional level, that affect innate host responses to M. tuberculosis. This underlines the importance of cellular metabolism for host immunity and supports a role for metformin as host-directed therapy for tuberculosis.

overall_design: Ex vivo blood RNA samples analyzed from 11 healthy donors, prior to administration of metformin (control) and after 5 days of metformin (test). Total 22 samples, with 11 clinical replicates.

first: Jacqueline

first: Clare

last: Eckold

first: Ekta

last: Lachmandas

first: Hazel

last: Dockrell

first: Mihai

middle: G

last: Netea

first: Reinout

last: van Crevel


title: NR4A3 plays a pivotal role in the differentiation of monocyte-derived dendritic cells

city: Montréal

first: Salix

last: Boulet

state: Québec

address: 5415 rue de l'assomption

country: Canada

institute: Centre de recherche de l'hôpital Maisonneuve-Rosemont

summary: The molecular requirements that guide the differentiation of monocytes into macrophages or monocyte-derived dendritic cells (Mo-DCs) are poorly understood. Here, we demonstrate that the nuclear orphan receptor NR4A3 guides monocyte fate and is essential for Mo-DC differentiation. Nr4a3-/- mice are impaired in the in vivo generation of DC-SIGN+ Mo-DCs following LPS stimulation and, as such, are defective at priming a CD8+ T cell response to gram negative bacteria. We also demonstrate that NR4A3 is an essential downstream effector of IRF4 during in vitro differentiation of Mo-DCs with GM-CSF and IL-4 and that, in absence of NR4A3, monocytes are diverted to macrophages. Our transcriptomic analysis of the genes regulated by NR4A3 reveals that the acquisition of the Mo-DC differentiation program is intertwined with the acquisition of a migratory signature. Furthermore, NR4A3 is critical for steady-state migration of non-lymphoid tissue conventional DCs to lymph nodes. Altogether, our results highlight a unique role for NR4A3 in Mo-DC differentiation and in the acquisition of migratory properties.

overall_design: Total RNA from sorted murine monocytes (see above) and from murine monocytes cultured with GM-CSF and IL-4 for 1 and 2 days (2 samples per group from 2 independent experiments) was isolated and sequenced with Illumina HiSeq2000.

first: Nathalie

last: Labrecque


title: LobSig a prognostic gene expression signature for invasive lobular carcinoma -Gene Expression Profiling

status: Public on Jun 17 2019

city: Brisbane

first: Peter

middle: T

last: Simpson

email: p.simpson@uq.edu.au, amy.reed@uq.edu.au

address: 71/918 RBWH Herston

department: Molecular & Cellular Pathology

country: Australia

institute: UQCCR

summary: Analysis of invasive lobular carcinoma (ILC) at gene expression level. Samples are annotated with breast cancer specific survival (BCSS) and tumour grade. Results are part of a larger study about molecular signatures that are associated with distinct clinical outcomes in ILC.

overall_design: Total RNA was extracted from fresh tumor tissues comprising ≥40% invasive tumor cells and hybridized on Illumina microarrays.

first: Amy

last: McCart Reed

first: Samir

last: Lal


title: Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2 [CHIP-Seq]

status: Public on Jun 18 2019

city: Munster

first: Veeramohan

last: Veerapandian

state: North Rhine-Westphalia

address: Röntgenstr. 20

department: Department Tissue Morphogenesis

institute: Max Planck Institute for Molecular Biomedicine

summary: Oct4, along with Sox2 and Klf4 (SK), can induce pluripotency but structurally similar factors like Oct6 cannot. To decode why Oct4 has this unique ability, we compare Oct4-binding, accessibility patterns and transcriptional waves with Oct6 and an Oct4 mutant defective in the dimerization with Sox2 (Oct4defSox2). We find that initial silencing of the somatic program proceeds indistinguishably with or without Oct4. Oct6 mitigates the mesenchymal-to-epithelial transition and derails reprogramming. These effects are a consequence of differences in genome-wide binding, as the early binding profile of Oct4defSox2 resembles Oct4, whilst Oct6 does not bind pluripotency enhancers. Nevertheless, in the Oct6-SK condition many otherwise Oct4-bound locations become accessible but chromatin opening is compromised when Oct4defSox2 occupies these sites. We find that Sox2 predominantly facilitates chromatin opening, whilst Oct4 serves an accessory role. Formation of Oct4/Sox2 heterodimers is essential for pluripotency establishment; however, reliance on Oct4/Sox2 heterodimers declines during pluripotency maintenance.

overall_design: We analyzed the genome binding  profiles of Oct4,Oct6, Oct4 mutant with two interface mutations leading to a disruption of the DNA dependent dimer with Sox2 (Oct4I21Y/D29R  in manuscript termed Oct4defSox2 and data in GEO is submitted by name "YR"), Oct4S151M mutant, and Oct6M151S mutant as well as Sox2 by ChIP-seq at different time point of retrovirus based somatic cell reprogramming to iPSC  in highly efficient chemically defined iCD1 medium.

first: Vikas

last: Malik

first: Ralf

last: Jauch


title: Prevention of chromatin destabilization by FACT is crucial for malignant transformation [gene expression]

status: Public on Jun 14 2019

city: Buffalo

first: Katerina

last: Gurova

state: NY

address: Elm and Carlton Str

department: Cell Stress Biology

institute: Roswell Park Cancer Institute

summary: Histone chaperone FACT is commonly expressed and essential for the viability of transformed but not normal cells and its expression levels correlate with poor prognosis in cancer patients. FACT binds several components of nucleosomes and has been viewed as a factor destabilizing nucleosomes to facilitate RNA polymerase passage. To connect FACT’s role in transcription with the viability of tumor cells, we analyzed genome-wide FACT binding to chromatin in conjunction with transcription in mouse and human cells with different degrees of FACT dependence. While genomic distribution and density of FACT correlated with the intensity of transcription, FACT knockout or knockdown was unexpectedly accompanied by the elevation, rather than suppression, of transcription and with the destabilization of chromatin.  These data suggest that the real function of FACT is to stabilize and reassemble nucleosomes disturbed by transcription. This function is apparently vital for tumor cells because malignant transformation is accompanied by chromatin destabilization.

overall_design: Mouse skin fibroblasts were isolated from tails of Ssrp1fl/fl;CreERT2+/+ mice. Primary cells were immortalized with p53 suppressive element GSE56 and transformed by GSE56+ HRasV12. To delete Ssrp1 cells were treated with hydroxytamoxifen for 5 days.

first: Jianmin

last: Wang


title: Metformin alters human host responses to Mycobacterium tuberculosis in-vitro and in healthy human subjects

first: Jackie

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

overall_design: Refer to individual Series


title: A Cystic Fibrosis Pseudomonas aeruginosa Isolate Specialised to Catabolise Nucleic Acids

city: Macquarie University

first: Anahit

last: Penesyan

state: NSW

address: E8A, Eastern road

institute: Mcquarie University

summary:
Purpose: Pseudomonas aeruginosa is a major cause of morbidity and mortality in patients with cystic fibrosis (CF). We provide an insight to the DNA auxotrophy of P. aeruginosa PASS4 isolate. Better understanding of P. aeruginosa adaptations in the CF lung environment can have a great impact in the development of specialised treatment regimes aimed at the eradications of P. aeruginosa infections.
Methods: P. aeruginosa strains PAO1 and PASS4 were grown in minimal medium with either L-Asparagine  or DNA as a carbon source, in biological triplicates. RNA was extracted and sequenced on Illumina HiSeq 1000 platform. The sequence reads that passed quality filters were analyzed  using EdgePro and DESeq packages, as well as the Rockhopper tool.
Results: We mapped > 10 million paired sequence reads per sample to the  genome of P. aeruginosa PAO1 and identified a total of 576 genes differentially expressed by PASS4 when grown in DNA (P value < 0.01, log2 fold-change 1< to < -1), with 322 genes upregulated and 254 genes downregulated. There were a total of 423 genes differentially expressed by PAO1 when grown in DNA (P value < 0.01, log2 fold-change 1< to <-1), with 359 genes upregulated and 64 genes downregulated . A total of 129 transcripts displayed similar expression patterns in both organisms, with 112 being upregulated and 17 down-regulated.
Conclusions: Our study identified that P. aeruginosa PASS4 was a purine auxotroph. Purine auxotropy may represent a viable microbial strategy for adaptation to DNA rich environments such as the CF lung.

overall_design: mRNA profiles of P. aeruginosa strains PAO1 and PASS4 grown in minimal media with either DNA or L-Asparagine as a sole carbon source were generated by paired end  sequencing, in triplicate, using Illumina HiSeq.

first: Sheemal

middle: S

last: Kumar


title: Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2


title: DNA Damage Signaling - induced Cancer Cell Reprogramming as a Driver of Tumor Relapse

status: Public on Jun 13 2019

city: Nice

first: Dmitry

last: Bulavin

address: 28 Av Valomdrose

country: France

institute: IRCAN

summary: Accumulating evidence supports the role of the DNA damage response (DDR) in the negative regulation of tumorigenesis. Previous data show that inactivation of WIP1 phosphatase, as a means of activating DDR signaling, delays tumor onset in multiple mouse models. Unexpectedly, we found that targeting WIP1 also accelerates tumor relapse. Through chromatin remodeling, DDR signaling poises the reactivation of early pluripotency genes, including OCT4A, contributing to tumor relapse. Redistribution of DNMT3B to heterochromatic sequences appears to be a key initiating event in DDR-dependent OCT4 locus reactivation. However, full reactivation requires the presence of a driving oncogene such as Myc and macroH2A downregulation, both of which are commonly present in advanced human cancers. Using genetic lineage tracing experiments, we further showed that Oct4a-expressing cells contributed to tumor relapse. Furthermore, conditional deletion of Oct4a was sufficient to significantly delay the relapse of myc-driven B-cell lymphomas. Here, we have uncovered an unexpected tumor-promoting role of DDR signaling in enforcing oncogene-induced tumor relapse by poising cancer cell reprogramming  into a stemness-like state. Our data support a model in which clonal evolution serves as an alternative organizational structure of certain tumors, such that nearly any cancer cell may acquire novel epigenetic traits to facilitate tumor relapse without necessarily committing to a Cancer Stem Cell model.

overall_design:
Gene expression analysis in human HCT116 cells (WT), WT treated with ATM inhibitor (WT+ ATMi), WIp1-depleted HCT116 cells with shRNA(SH) and SH treated with ATM inhibitor (SH + ATMi).
Total RNA was purified from indicated cancer cell lines of 3 different biological replicate for each cell line, to assess differently expressed genes beween all cell line analyzed

first: Doria

last: Filipponi


title: Identification of the coiled-coil domain as an essential element of MBD3 for preserving lineage commitment potential of ESCs

first: Akihiko

last: Okuda

summary: As one of approaches for elucidating the molecular bases which define the difference for counteracting defect of Mbd3-knockout ESCs between MBD3a mutant lacking MBD domain and that lacking coiled-coil domain, we explored the possibility that these two mutants are different in their ability to recruit PRC2 complex in close vicinity by ChIP-sequence analyses.

overall_design: To inquire how SUZ12 binding genomic sites are globally affected dependently on the kinds of MBD3 mutants, ChIP-sequence analyses were conducted with antibody against SUZ12 using Mbd3-knockout ESCs which bear a MBD3a mutant lacking either MBD or coiled-coil domains.

first: Masataka

last: Hirasaki

first: Masakazu

last: Kohda

first: Yasushi

last: Okazaki


title: Prevention of chromatin destabilization by FACT is crucial for malignant transformation

status: Public on Jun 12 2019


title: Genome-wide gene expression analysis for co-induction of ISH1 and ISH2 in the Arabidopsis

city: Kisarazu

first: Shigeru

last: Hanano

state: Chiba

address: 2-6-7 Kazusa-Kamatari

department: Department of Frontier Research and Development

institute: Kazusa DNA Research Institute

summary:
Co-induction of both ISH1 and ISH2 produces stem-like greening organs in the Arabidopsis root. To elucidate the target genes regulated by ISH1 and ISH2, individual ISH1 or ISH2, or both ISH1 and ISH2 were chemically induced under LexA operator in the Arabidopsis Col-0.
Gene expressions were compared among the samples to investigate the regulated genes in ISH1- and ISH2- induced plants.

In the citation, the ISH1 and ISH2 correspond to ATHB25 (Ag5g65410) and REM7 (At3g18960), respectively.

overall_design: Control, ISH1-ind, ISH2-ind and ISH1&2-ind plants were generated. Each seedling was treated with/or without an estradiol and the root samples were harvested. A total of 24 samples (4 types of plants x 2 w/o treatments x 3 biological triplicates) were analyzed by Agilent-021169 Arabidopsis 4 Oligo Microarray (V4).

first: Hajime

last: Tomatsu

first: Kunihiro

last: Suda

first: Tsutomu

last: Hosouchi

first: Hideyuki

last: Suzuki

first: Nozomu

last: Sakurai

first: Daisuke

last: Shibata


title: Replication-independent histone turnover confers regulatory genome for adult heart homeostasis [ChIP-Seq]

city: Irvine

first: Yumei

last: Li

address: 825 Health Sciences Road

department: Department of Biological Chemistry

institute: University of California, Irvine

summary: Disruption and replacement of nucleosomal histone (histone turnover, HT) take place during transcription and cell division. Here we examined the functional roles for replication-independent HT in directing precise regulatory genome in terminally differentiated cardiomyocytes (CMs) of adult heart. Surprisingly, histone H2B pausing and chasing assay revealed the histone halftime ~2.5 weeks in non-replicating CMs, in sharp contrast to the longer halftime of CMs, despite in the abscence of replication-dependent passive dilution of labeled histones. Regions of high HT identified enhancers of important heart function. Co-occupancy of mutiple cardiac transcription factors in part accounted for enhancers on sites lacking nucleosome eviction by passage of RNA polymerase II. Unexpectedly, both polycomb EED and HDACs augmented HT rate in bufferring poised enhancer activition without alteration of nucleosome occupancy. Thus, our results suggest replication-indenpendent HT as an additional layer of chromatin-based regulation of functional homeostasis.

overall_design: GFP-tagged H2B occupancy profile in isolated adult cardiomyocytes from Wildtype (WT) at 6 time points and in cardiac conditional EED Knockout (CKO) at 2 time points as well as nucleosome profile in CKO and WT.

first: Shanshan

last: Ai

first: Chen

first: Xianhong

last: Yu

first: Xin

first: Yanzhu

last: Yue

first: Cheng

first: William

last: Pu

first: Chuanyun

first: Aibin

last: He


title: Replication-independent histone turnover confers regulatory genome for adult heart homeostasis


title: TNF-induced gene-expressions in Nfkb2-/- MEFs and its derivatives

city: New Delhi

first: Soumen

last: Basak

state: Delhi

address: Aruna Asaf Ali Marg

department: Infection and immunity

country: India

institute: National Institute of Immunology

summary: As such, TNF triggers the canonical NF-?B pathway to induce a nuclear NF-?B activity composed of the RelA:p50 dimer in WT cells. Nfkb2 encodes p100, which regulates the activity of the RelB NF-?B heterodimers during immune cell-differentiation via the noncanonical pathway. Our biochemical analyses revealed that an absence of p100 instead repositions RelB under the control of the TNF-activated canonical pathway. Indeed, chronic TNF treatment of Nfkb2-/- cells activates the RelA:p50 dimer and an additional RelB:p50 dimer.  On the other hand, TNF stimulation of Relb-/-Nfkb2-/- and Rela-/-Nfkb2-/- MEFs exclusively activated the RelA:p50 dimer and the RelB:p50 dimer, respectively. We treated this panel of knockout MEFs with TNF for 6h before being subjected to microarray mRNA analysis. We also included in our analysis WT MEFs and Rela-/-Relb-/-Rel-/- MEFs, which served as a negative control. Our analyses revealed overlapping and distinct gene-expression specificities of RelA:p50 and RelB:p50 dimers activated in mutant cells in response to TNF.

overall_design: Total RNA isolated from biological replicate samples comprising of untreated and 6h TNF (10ng/ml) treated WT, Nfkb2-/-, Rela-/-Nfkb2-/-, Relb-/-Nfkb2-/-and Rela-/-Relb-/-Rel-/- MEFs were analyzed for global gene expression levels

first: S

first: P

last: Roy

first: B

last: Chatterjee

first: U

last: Sarkar


title: WNK1 kinase and the termination factor PCF11 connect nuclear mRNA export with transcription

city: Oxford

first: Monika

last: Gullerova

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

summary: Transcription termination and mRNA export from the nucleus are closely regulated and coordinated processes. Nuclear export factors are recruited to actively transcribed genes through their interactions with protein complexes associated with transcription and co-transcriptional pre-mRNA processing. We determine a new role for the kinase WNK1 in the cross-talk of transcription termination and mRNA export.  WNK1 was previously attributed a cytoplasmic role as a regulator of ion transport. However, we now show a nuclear function for this kinase where it is required for efficient mRNA export along with the transcription termination factor PCF11. Finally, we identify the phosphorylation of the CID domain of PCF11 as an important step for the release of the mRNA from the transcription locus, thus allowing efficient mRNA export to the cytoplasm.

overall_design: RNA from cytoplasmic and nuclear extracts of HeLa cells was obtained, upon depletion of WNK1 kinase or from control cells. Upon pA selection, libraries were generated and sequenced. A duplicate experiment was performed for each sample.

first: Adam

last: Volanakis

first: Kinga

last: Kamieniarz-Gdula

first: Margarita

last: Schlackow

first: Nicholas

last: Proudfoot


title: Comparison of 7 small cell lung cancer PDX models, cultured ex vivo, for response to LSD1 inhibitor RG6016/ORY1001

status: Public on Jun 10 2019

city: Seattle

first: David

last: MacPherson

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

summary: The goal of this study was to understand how the LSD1 inhibitor RG6016/ORY1001 leads to selective efficacy in subsets of small cell lung cancer. SCLC cell lines, PDX models studied ex vivo and studied in vivo were employed in this analysis

overall_design: SCLC PDX models were transiently cultured and exposed to saline vehicle or 1nM RG6016/ORY1001 for 48 hours. RNA was isolated and RNA-seq analyses performed

first: Arnaud

last: Augert


title: Comparison of small cell lung cancer PDX model FHSC04 for response to LSD1 inhibitor RG6016/ORY1001

overall_design: SCLC PDX model was propagated into 10 immunocompromised NSG mice. 5 were treated with saline vs. 5 with 400ug/kg RG6016/ORY1001 orally on day 0,7 and 4 hours before collection on Day 10. Tumor RNA was isolated and RNA-seq analyses performed


title: Expression data from mouse precision cut lung slices (PCLS) after human rhinovirus (RV) infection and after treatment with bronchobini (BRO).

city: Hannover

first: Stella Marie

last: Reamon-Buettner

address: Nikolai-Fuchs Strasse1

department: Preclinical Pharmacology & In Vitro Toxicology

institute: Fraunhofer-ITEM

summary:
Transcriptome analysis revealed a robust and multifactorial mode of action of BRO. BRO suppressed RV induced responses, e.g. upregulation of the antiviral interferon (IFN) signaling pathway, while stimulating this pathway under baseline conditions.
Suppression of RV-induced cytokine release and downregulation of IFN signaling pathway confirmed that BRO exerts a beneficial anti-inflammatory effect during viral infection.

overall_design: Mouse PCLS containing airways were prepared from BALB/c mice. For each experiment PCLS from three mices were pooled. Mouse PCLS were pre-incubated with BRO in three different doses or BRO vehicle. Afterwards mPCLS were infected with RV, replicative deficient UV-RV or medium as sham infection. mPCLS samples were used for RNA isolation and gene expression analysis.

first: Stella

last: Niehof

first: Sabine

last: Wronski


title: Small cell lung cancer PDX model response to LSD1 inhibitor RG6016/ORY1001


title: Metformin alters human host responses to Mycobacterium tuberculosis in-vitro and in healthy human subjects [PBMC RNA-Seq]

first: Jackie

last: Cliff

summary: Metformin, the most widely administered diabetes drug, has been proposed as a candidate for host directed therapy for tuberculosis although very little is known about its effects on human host responses to Mycobacterium tuberculosis. When added in vitro to PBMCs isolated from healthy non-diabetic volunteers, metformin increased glycolysis, inhibited the mTOR targets, strongly reduced M. tuberculosis induced production of TNF-alpha (-58%), IFN-gamma (-47%) and IL-beta (-20%), while increasing phagocytosis. In healthy subjects, in vivo metformin intake induced significant transcriptional changes in whole blood and isolated PBMCs, with substantial down-regulation of genes related to inflammation and the type 1 interferon response. Metformin intake also increased monocyte phagocytosis (by 1.5 to 2 fold) and ROS production (+20%). These results show that metformin in humans has a range of potentially beneficial effects on cellular metabolism, immune function and gene-transcriptional level, that affect innate host responses to M. tuberculosis. This underlines the importance of cellular metabolism for host immunity and supports a role for metformin as host-directed therapy for tuberculosis.

overall_design: Peripheral Mononuclear Cells taken from 11 healthy donors, prior to administration of metformin and after 5 days of metformin. Samples were stimulated with Mycobacterium tuberculosis lysate or cultured unstimulated for 4 hours. Total 88 samples, with 11 clinical replicates.

first: Jacqueline

first: Clare

last: Eckold

first: Ekta

last: Lachmandas

first: Hazel

last: Dockrell

first: Mihai

last: Netea

first: Reinout

last: van Crevel


title: Toxicity mechanisms of ZnO UV-filters used in sunscreens toward the model cyanobacteria Synechococcus elongatus PCC7942

status: Public on Jun 05 2019

city: METZ

first: Bénédicte

last: SOHM

address: 8 rue du Gal Delestraint

institute: CNRS

summary: Zinc oxide (ZnO) nanoparticles are commonly used in sunscreens for their UV-filtering properties. Their growing use can lead to their release into ecosystems, raising question about their toxicity. Effects of these engineered nanomaterials (ENMs) on cyanobacteria, which are important primary producers involved in many biogeochemical cycles, are unknown. In this study, we investigated by several complementary approaches the toxicological effects of two marketed ZnO-ENMs (coated and uncoated) on the model cyanobacteria Synechococcus elongatus PCC 7942. It was shown that despite the rapid adsorption of ENMs on cell surface, toxicity is mainly due to labile Zn released by ENMs. Zn dissipates cell membrane potential necessary for both photosynthesis and respiration, and induces oxidative stress leading to lipid peroxidation and DNA damages. It leads to global downregulation of photosystems, oxidative phosphorylation, and transcription/translation machineries. This also translates into significant decrease of intracellular ATP content and cell growth inhibition. However, there is no major loss of pigments and even rather an increase in exposed cells compared to controls. A proposed way to reduce the environmental impact of Zn would be the improvement of the coating stability to prevent solubility of ZnO-ENMs.

sample_organism: Synechococcus elongatus PCC 7942 = FACHB-805

overall_design: Synechococcus elongatus PCC 7942 cells were exposed to 5 mg/L of either Z-COTE or Z-COTE HP1 or ZnCl2 or solvent control in EPA Very Soft Water (VSW ; pH 6.4 ± 0.3)  with 4 replicates for each condition. Cells were incubated 5 h at 20 °C under 100 rpm agitation and continuous light. Microarray approaches were used to investigate global molecular response of the cyanobacteria exposed to coated (Z-COTE HP1) and uncoated (Z-COTE) zinc oxide nanomaterials. Results were also compared to those obtained with the Zn ionic forms.

first: Christophe

last: Pagnout

first: Anne

last: Vicente

first: Pascale

last: Bauda

first: Justine

last: Flayac

first: Philippe

last: Rousselle


title: Replication-independent histone turnover confers regulatory genome for adult heart homeostasis [Mnase-Seq]

first: Yumei

last: Li

first: Shanshan

last: Ai

first: Chen

first: Xianhong

last: Yu

first: Xin

first: Yanzhu

last: Yue

first: Cheng

first: William

last: Pu

first: Chuanyun

first: Aibin

last: He


title: GLI2-mediated mesenchymal Hh signaling induces stem cell niche signals in intestinal development and tumorigenesis [RNASeq]

status: Public on Jun 04 2019

city: Toronto

first: Tae-Hee

last: Kim

state: Ontario

address: 686 Bay Street. Room 16.9709

department: Developmental & Stem Cell Biology

institute: The Hospital for Sick Children

summary: Mesenchymal-epithelial interactions play a critical role in organ development, stem cells and disease. During intestinal development, pseudostratified epithelia undergo dramatic morphogenesis called villification, to form finger-like projections, in which mesenchymal cell clustering and muscle layers play a key role. In the adult, the gut mesenchyme is proposed as a key intestinal stem cell niche providing essential niche signals such as Wnt ligands, while the TGF beta signaling mediated gut stromal program is critical for cancer progression. However, how these signals are produced is currently unknown. In the gut, Hedgehog (Hh) signaling acts strictly in a paracrine manner: Hh ligands are expressed in the epithelium and activate signaling exclusively in the mesenchyme. Notably, Hh signaling is not only essential for mesenchymal clustering and muscle differentiation, it is also involved in intestinal tumorigenesis. To investigate Hh mediated mechanisms, we analyzed mice deleted for key Hh negative regulators, Sufu and/or Spop in the gut mesenchyme, and demonstrated their dosage dependent role in the negative regulation of Hh signaling. Although these mutants exhibit abnormal mesenchymal cell growth and functionally defective muscle layers, villification is completed with proper mesenchymal clustering, implying a permissive role for Hh signaling. These mesenchymal defects are partially rescued by Gli2 reduction, demonstrating the significance of its transcriptional regulation. Surprisingly, in contrast to its known inhibitory role in epithelial proliferation, abnormal Hh activation in the gut mesenchyme leads to increased epithelial proliferation. Corroborating this data, Sufu reduction is sufficient to promote intestinal tumorigenesis, while Gli2 heterozygosity suppresses it. To define GLI2-mediated downstream mechanisms, we mapped its binding sites and analyzed gene expression genome-wide, identifying one of the most robust Hh direct targetome data sets ever reported. This work reveals the GLI2 transcriptional regulation of Wnt and TGF beta pathways in stem cell proliferation and muscle differentiation, providing mechanistic insight into the intestinal stem cell niche in development and tumorigenesis.

overall_design: RNA-Seq of E17.5 wildtype and Sufu;Spop double knockout intestine in biological duplicates

first: Sabrina

last: Coquenlorge-Gallon

first: Wen-Chi

last: Yin


title: GLI2-mediated mesenchymal Hh signaling induces stem cell niche signals in intestinal development and tumorigenesis


title: A genome-wide approach to delineate novel XBP-1 targets involved in liver metabolism

status: Public on Jun 03 2019

city: Nanjing

first: Zhenji

last: Gan

address: 12 Xuefu Road

department: Model Animal Research Center of Nanjing University

institute: Nanjing University

summary:
This experiment was conducted to identify novel XBP-1 targets involved in liver metabolism. The following abstract from the submitted manuscript describes the major findings of this work.

The IRE1a-XBP1s axis regulates the COPII-mediated secretory program in response to nutrient availability. Lin Liu, Jie Cai, Xijun Liang, Qian Zhou, Huimin Wang, Chenyun Ding, Yuangang Zhu, Liwei Xiao, Tingting Fu, Zhisheng Xu, Jing Liu, Yujing Yin, Lei Fang, Bin Xue, Yan Wang, Aibin He, Yong Liu, Xiao-Wei Chen, and Zhenji Gan

The cytoplasmic coat protein complex-II (COPII) is an evolutionarily conserved machinery that is essential for efficient trafficking of protein and lipid cargos. How the COPII machinery is regulated to meet the metabolic demand in response to alterations of nutritional state remains largely unexplored, however. Here, we show that dynamic changes of COPII-mediated secretion parallel the activation of XBP1s, the critical transcription factor in handling cellular ER stress, in both live cells and mouse liver upon physiological fluctuations of nutrient availability. Using live-cell imaging approaches, we demonstrate that XBP1s is sufficient to promote COPII-dependent secretion, mediating the nutrient stimulatory effects. ChIP-seq and RNA-seq analyses reveal that nutritional signals induce dynamic XBP1s occupancy of promoters of COPII secretion-related genes, thereby driving COPII-directed secretory process. Liver-specific disruption of the IRE1a-XBP1s signaling branch results in diminished COPII-mediated secretion. Reactivation of XBP1s in mice lacking hepatic IRE1a restores COPII-mediated lipoprotein secretion, and reverses the fatty liver and hypolipidemia phenotypes. Thus, our results demonstrate a previously unappreciated mechanism in the metabolic control of liver protein and lipid secretion: the IRE1a-XBP1s axis functions as a nutrient-sensing regulatory nexus that integrates nutritional states and the COPII secretory program.

overall_design: Using genome-wide approach, ChIPseq, to delineate novel XBP-1 targets involved in liver metabolism

first: Qian

last: Zhou

first: Xijun

last: Liang

first: Lin

last: Liu


title: Cell cycle dependent regulation and function of Argonaute 1 in plants

status: Public on Jun 06 2019

city: Davis

first: Patricia

last: Baldrich Gonzalez

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

type: Non-coding RNA profiling by high throughput sequencing


title: Cell cycle dependent regulation and function of Argonaute 1 in plants [PARE]

summary: The RNA silencing (RNAi) is a biological process, which plays a key role in a wide range of eukaryotes, such as gene expression regulation, transposable elements control and antiviral defense. In human, several studies showed that miRNAs and AGO2 are involved in the regulation of the cell cycle. Indeed, many cell cycle regulators such as cyclins, CDKs, CDK inhibitors, RBR proteins or E2F transcription factors have been identified as miRNA targets. Transcriptional data suggest that these cell cycle miRNAs are differentially accumulated during cell cycle progression and that misregulation of some could lead to proliferative diseases. However, in plants, almost nothing is known about the cell cycle regulation through miRNAs. Unpublished datas from the lab suggest that the Arabidopsis AGO1, which is the most important Argonaute for miRNA-mediated gene regulation, is essential for cell proliferation. In order to investigate the role of AGO1 during cell cycle, we set up a system based on cell cycle synchronization of tobacco BY-2 cell suspensions expressing a GFP-fused AGO1. We sequenced small RNAs from S, G2, M and G1 phases of synchronized cells from total RNA extract and GFP-AGO1 co-purified small RNAs, and investigate whether putative cell cycle specific miRNAs can be highlighted.

overall_design: 3 different replicates of PARE libraries from total RNA are included in this study. They correspond to 4 different phases of the cell cycle.

last: Baldrich

first: Adrien

last: Trolet

first: Marie

last: Criqui

first: Marion

last: Clavel

first: Pascal

last: Genschik

first: Blake

last: Meyers


title: Cell cycle dependent regulation and function of Argonaute 1 in plants [small RNA-seq]

overall_design: 5 different replicates of small RNA-seq from AGO1IP and total RNA are included in this study. They correspond to 4 different phases of the cell cycle.


title: A natively unstructured RNA/protein-recognition core in the E. coli RNA degradosome facilitates riboregulation

status: Public on Jun 01 2019

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: The RNA degradosome is a multi-enzyme assembly that plays a central role in the RNA metabolism of Escherichia coli and numerous other bacterial species including pathogens. The core of the assembly is provided by the endoribonuclease RNase E, one of the largest E. coli proteins. The C-terminal half of RNase E is predicted to be predominantly unstructured and is punctuated with conserved short linear motifs that recruit partner proteins, direct RNA interactions, and enable association with the cytoplasmic membrane.  We demonstrate that a subassembly of the degradosome - comprising a 248-residue segment of the C-terminal part of RNase E, the DEAD-box helicase RhlB, and the glycolytic enzyme enolase - serves as a flexible recognition centre that can co-recruit small regulatory RNA (sRNA) molecules and the RNA chaperone Hfq into an effector complex. The association of enolase with the degradosome impacts on carbon utilisation pathways under changing metabolic conditions, most likely by facilitating recruitment and the activity of sRNAs. Our results support a model in which the degradosome captures substrates and regulatory RNAs through the recognition core, facilitates pairing to cognate transcripts, and presents the target to the ribonuclease active sites of the greater assembly for cooperative degradation or processing.

overall_design: In order to compensate specific effects of the dyes and to ensure statistically relevant data analysis, a color-swap dye-reversal was performed. Ratio profiles comprising single hybridizations were combined in an error-weighted fashion to create ratio experiments. A 1.5-fold change expression cut-off for ratio experiments was applied together with anti-correlation of color-swapped ratio profiles was applied, rendering the microarray analysis highly significant (P-value > 0.01), robust and reproducible.

first: Kai

last: Papenfort


title: Fast evolution of gained essential function by a young gene through gained interaction with other essential genes [ChIP-Seq]

first: Grace

middle: Yuh Chwen

last: Lee

address: UCI

summary: New genes are those that originated relatively recently and are only present in a subset of species in a phylogeny. Evidence from humans and other species has demonstrated that, despite their young age, new genes can exhibit novel functions that are essential for the survival of an organism. One potential mechanism by which new genes gain essential functions is through the acquisition of many new interactions with pre-existing genes. This hypothesis is consistent with well-established observations that genes with many interaction partners are more likely to have essential functions. However, the accumulation of gene-gene interactions is, on average, a slow evolutionary process. This raises the question of how, in a short evolutionary time, new genes can acquire multiple novel interactions and how this might lead to their essential roles in the survival of an organism. In this study, we characterized the evolutionary history and function of a young duplicated gene that quickly became essential for the survival of Drosophila melanogaster. This young gene (CG7804) duplicated from another essential gene (TBPH) through retrotransposition less than four million years ago (Zhang et al. 2010), and is present in few Drosophila species. We found that unlike its evolutionarily conserved, broadly expressed parental gene, CG7804 has evolved rapidly under positive selection since its birth. Despite its young age, functional analyses show that CG7804 is essential for the survival of D. melanogaster. In particular, its expression is essential at different tissues from its parental gene. RNA-seq and ChIP-seq analysis suggests that CG7804 acquired essential function to survival through gaining new DNA binding targets that influence the expression of a suite of genes with other essential function and large number of protein-protein interaction. Our study is an important step towards deciphering the evolutionary trajectory by which duplicated genes functionally diverge from the parental gene and become essential.

overall_design: ChIP-Seq of transgenic strains with GFP-tagged CG7804 or TBPH

middle: Y

first: Manyuan

last: Long


title: GLI2-mediated mesenchymal Hh signaling induces stem cell niche signals in intestinal development and tumorigenesis [ChIPSeq]

first: Tae-Hee

last: Kim

overall_design: Examination of Gli2, H3K27ac, and H3K36me3-bound DNA in E17.5 Sufu;Spop double knockout mouse intestine

last: Coquenlorge-Gallon


title: Early response to loss of Argonaute proteins in embryonic stem cells activates the Tgf-ß/Smad Transcriptional Network [ChIP-Seq]

city: LOS ANGELES

first: Jesse

middle: R

last: Zamudio

address: 610 CHARLES E. YOUNG DRIVE EAST BOX 957239

department: MCDB

institute: University of California, Los Angeles

summary: Argonaute (Ago) proteins, which act in post-transcriptional gene regulation directed by small RNAs, are vital for normal stem cell biology. Here we report the genomic characterization of stable Ago-deficient mouse embryonic stem cells (mESC) and determine the direct and system level response to loss of Ago-mediated regulation. We find mESCs lacking all four Ago proteins are viable, do not repress microRNA (miRNA)-targeted cellular RNAs, and show distinctive gene network signatures. Profiling of RNA expression and epigenetic activity in an Ago mutant genetic series indicates that early responses to Ago loss are driven by transcriptional regulatory networks, in particular the Tgf-ß/Smad transcriptional network. This finding is confirmed using a time course analysis of Ago depletion and Ago rescue experiments. Detailed analysis places Tgf-ß/Smad activation upstream of cell cycle regulator activation, such as Cdkn1a, and repression of the c-Myc transcriptional network. The Tgf-ß/Smad pathway is directly controlled by multiple low-affinity miRNA interactions with Tgf-ß/Activin receptor mRNAs and receptor-mediated activation is required for Tgf-ß/Smad target induction with Ago loss. Our characterization reveals the interplay of post-transcriptional regulatory pathways with transcriptional networks in maintaining cell state and likely coordinating cell state transitions.

overall_design: ChIP seq from stable genetic Ago mutant mouse embryonic stem cells.


title: hnRNPC regulates cancer-specific alternative cleavage and polyadenylation profiles

city: Cambridge

first: Harry

last: Fischl

address: Babraham Research Campus

institute: Storm Therapeutics

summary: Alternative cleavage and polyadenylation (APA) can occur at more than half of all human genes, greatly enhancing the cellular repertoire of mRNA isoforms. As these isoforms can have altered stability, localisation and coding potential, deregulation of APA can disrupt gene expression and this has been linked to many diseases including cancer progression. How APA generates cancer-specific isoform profiles and what their physiological consequences are, however, is largely unclear. Here we use a subcellular fractionation approach to determine the nuclear and cytoplasmic APA profiles of successive stages of colon cancer using a cell line-based model. Using this approach, we show that during cancer progression specific APA profiles are established. We identify that overexpression of hnRNPC has a critical role in the establishment of APA profiles characteristic for metastatic colon cancer cells, by regulating poly(A) site selection in a subset of genes that have been implicated in cancer progression including MTHFD1L.

overall_design: RNA was extracted from nuclear and cytoplasmic subcellular fractions from two biological replicates of the following cell lines: the non-malignant adult-derived human male colonic epithelial 1CT cell line and the SW480 and SW620 cell lines, which both derive from the same patient. The SW480 cell line was established from a Dukes’ type B primary adenocarcinoma of the colon and the SW620 cell line was derived from a lymph node after cancer recurred with widespread metastasis. The 3’ ends of extracted RNA were generated into libraries using the QuantSeq 3’mRNA-Seq library kit (Lexogen). Libraries were processed on the Ion Chef platform and subsequently sequenced on the Ion Proton system. Sequences were aligned using the Ion Torrent Server TMAP aligner to genome build hg19. RNA was also extracted from nuclear and cytoplasmic subcellular fractions from two biological replicates in SW620 cells following siRNA knockdown of HNRNPC, ELAVL1, or a control knockdown using scrambled siRNA. The 3’ ends of extracted RNA were processed and sequenced as before.

first: Jonathan

last: Neve

first: Zhiqiao

last: Wang

first: Radhika

last: Patel

first: Alastair

last: Louey

first: Bin

last: Tian

first: Andre

last: Furger


title: Gene expression analysis of WT and Adam19KO cardiac neural crest cells

city: Kyoto

first: Atsuko

last: Sehara-Fujisawa

state: 京都府

address: Department of Growth Regulation,, Institute for Frontier Medical Sciences, Kyoto Univ.,

institute: Inst. for Frontier Life and Med. Sci., Kyoto University

summary: Neural crest cells (NCCs) migrate into the heart, and their defects lead to congenital heart diseases. Despite the importance of cardiac NCCs (CNCCs), their final fates and underlying mechanisms of the fate specification have been unknown. Here we report that CNCCs differentiate from bipotent progenitors to tenocytes by preventing chondrogenesis. CNCCs highly express a disintegrin and metalloprotease 19 (Adam19) after migrating into the heart. Adam19-deleted CNCCs fail to suppress expression of Sox9 and generate abnormal cartilage, while they normally form the tendon connecting the aorta and pulmonary artery. Highly expressed Sox9 in CNCCs is necessary and sufficient for their chondrogenic fate decision. Adam19 inhibits response to BMP, preventing CNCCs from enhanced Sox9 expression. Our study reveals a novel fate of the NCC, and moreover, provides insights into how postmigratory NCCs define their fates locally.

overall_design: E14.5 Cardiac neural crest cells (CNCCs) were isolated from Adam19+/+; Wnt1-Cre; R26tdTomato/+ and Adam19-/-; Wnt1-Cre; R26tdTomato/+ embryonic hearts using FACS. Total RNA of sorted CNCCs were extracted with RNeasy micro Plus Kit(Qiagen). Mouse Gene 1.0 ST Array(Affymetrix) was used to compare Adam19+/+ CNCCs and Adam19-/- CNCCs.

first: Hiroyuki

last: Arai

first: Takuya

last: Yamamoto


title: c-MYC drives neuroblastoma tumorigenesis and retinoic acid resistance in zebrafish

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

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

overall_design: Refer to individual Series


title: Gene expression in THP-1 cells treated for 6 hours with CNT and GNP, conjugated with Indolicidin, Indolicidin spiked as well as free Indolicidin: Reference (Total RNA Mixture of all samples) vs. treated cells

status: Public on May 31 2019

city: Bhubaneswar

first: Biswaranjan

last: Pradhan

state: ODISHA

address: Jatni

department: Biological Sciences

institute: National Institute of Science Education and Research Bhubaneswar

summary: Transcriptional profiling of THP-1 cells on treatment with Indolicidin and nano conjugated Indolicidin.

overall_design: Twelve conditions of the expriment, Untreated THP-1 cells (NT) vs. treatment with free Indolicidin, free nano materials, and nano materials spiked with Indolicidin for 6 hours. Biological replicates: 3 in each case (Equal amount of total RNA from each replicate pulled together for microarray).

first: Pradhan

last: Biswaranjan

first: Sur

last: Abhinav

first: Aich

last: Palok


title: Gene expression in Raw264.7 Cells following treatment with probiotics strains Lactobacillus acidophilus, Bacillus clausii and Bifidobacterium bifidum at MOI of 1 for 6 hours : NT (Time matched untreated cells) vs. Probiotics treated cells

summary: Gene expression in RAW 264.7 cells on treatment with Lactobacillus acidophilus, Bacillus clausii and Bifidobacterium bifidum at MOI of 1 for 6 hours.

overall_design: Four conditions of the expriment, Untreated RAW 264.7 cells (NT) vs. treatment with Lactobacillus acidophilus, Bacillus clausii and Bifibacterium bifidum separately at MOI of 1 for 6 hours. Biological replicates: 3 in each case.

first: Dwivedy

last: Abhisek


title: Dynamic Change of Transcription Pausing through Modulating NELF Protein Stability Regulates Granulocytic Differentiation

city: Dallas

first: Xiaoying

last: Bai

state: TEXAS

address: 5323 Harry Hines Blvd.

department: OB/GYN

institute: UT Southwestern Medical Center

summary: The NELF complex is a metazoan-specific factor essential for establishing transcription pausing. Although NELF has been implicated in cell fate regulation, the cellular regulation of NELF and its intrinsic role in specific lineage differentiation remains largely unknown. Using mammalian hematopoietic differentiation as a model system, here we identified a dynamic change of NELF-mediated transcription pausing as a novel mechanism regulating hematopoietic differentiation. We found a sharp decrease of NELF protein abundance during granulocytic differentiation with a consequent genome-wide reduction of transcription pausing. This loss of pausing coincides with activation of granulocyte-affiliated genes and diminished expression of progenitor markers.  Functional studies revealed that sustained expression of NELF inhibits granulocytic differentiation, whereas NELF depletion in progenitor cells leads to premature differentiation towards the granulocytic lineage. Our results thus uncover a previously unrecognized regulation of transcription pausing by modulating NELF protein abundance to control cellular differentiation.

overall_design: using Gro-seq to analyze transcription in NELF-knockdown human CD34+ HSPCs and early differentiated granulocytes

first: Xiuli

last: Liu

first: Aishwarya

last: Gogate

first: Melodi

last: Tastemel

first: Venkat

last: Malladi

first: Huiyu

last: Yao

first: Kim

last: Nguyen

first: Lily

last: Huang


title: Gene expression in THP-1 Cells following treatment with probiotics strains Lactobacillus acidophilus, Bacillus clausii and Bifidobacterium bifidum at MOI of 1 for 6 hours : NT (Time matched untreated cells) vs. Probiotics treated cells

summary: Gene expression in THP-1 cells on treatment with Lactobacillus acidophilus, Bacillus clausii and Bifidobacterium bifidum at MOI of 1 for 6 hours.

overall_design:
Four conditions of the expriment, Untreated THP-1 cells (NT) vs. treatment with Lactobacillus acidophilus, Bacillus clausii and Bifibacterium bifidum separately at MOI of 1 for 6 hours. Biological replicates: 3 in each case.
Please ntoe that THP-1 cell line, originated from peripheral blood monocyte of an 1 year old human infant, was purchased from NCCS, India


title: c-MYC drives neuroblastoma tumorigenesis and retinoic acid resistance in zebrafish [ATAC-Seq]

summary: Neuroblastoma is an often intractable tumor that accounts for 15% of childhood cancer deaths. In addition to MYCN amplification in 20% of tumors, 11% express high levels of c-MYC (MYC) protein. To study this newly defined subgroup, we have created a novel transgenic zebrafish model in which overexpression of MYC in the peripheral sympathetic nervous system drives early-onset neuroblastoma.

overall_design: ATAC-seq was performed on MYC and MYCN driven neuroblastoma tumors to determine chromatin accesibility in these cells

first: Song

last: Yang

first: Yi

last: Zhou

middle: I

first: Mark

middle: W

last: Zimmerman

first: Shuning

last: He

first: Adam

middle: D

last: Durbin

first: A

last: Look

first: Amish

last: Khan

first: Xiaoling

last: Zhang

first: Shizhen

last: Zhu

first: Yu

first: Jinghui


title: Clinical and biological impact of miR-18a expression in breast cancer after neoadjuvant chemotherapy

status: Public on May 27 2019

city: Cartagena

first: Ginés

last: Luengo-Gil

address: C/ Mezquita s/n. 1ª planta

department: Department of Pathology

institute: UCAM

summary:
Purpose
The analysis of breast cancer residual tumors after neoadjuvant chemotherapy (nCT) may be useful for identifying new biomarkers. MicroRNAs are known to be involved in oncogenic pathways and treatment resistance of breast cancer. Our aim was to determine the role of miR-18a, a member of the miR-17-92a cluster, in breast cancer behavior and outcome after nCT.

Methods
Pre- and post-nCT tumor miR-18a expression was retrospectively assessed by qRT-PCR in 121 patients treated with nCT and was correlated with survival outcomes and with clinical and pathological characteristics. Breast cancer-derived MCF-7 and MDA-MB-231 cell lines were transfected with miR-18a and anti-miR-18a to evaluate the biological effects of this molecule. In addition, whole-transcriptome expression analysis was performed.

Results
High miR-18a expression in post-nCT residual tumors was found to be associated with a significantly worse overall survival [hazard ratio (HR): 2.80, 95% confidence interval (CI): 1.01–7.76] and a strong trend towards a poorer disease-free survival (HR: 2.44, 95% CI: 0.99–5.02) compared to low miR-18a expressing post-nCT residual tumors. Clinical and experimental data were found to be in conformity with the proliferative effects of miR-18a, which showed a significant correlation with Ki67 and MYBL2 expression, both in pre- and post-nCT tumors and in public databases. In vitro analysis of the role of miR-18a in breast cancer-derived cell lines showed that a high expression of miR-18a was associated with a low expression of the estrogen receptor (ER), a decreased sensitivity to tamoxifen and an enrichment in luminal B and endocrine resistance gene expression signatures.

Conclusions
From our data we conclude that post-nCT miR-18a expression in breast cancer serves as a negative prognostic marker, especially in luminal tumors. Clinical, in vitro and in silico data support the role of miR-18a in breast cancer cell proliferation and endocrine resistance and suggest its potential utility as a biomarker for additional adjuvant treatment in patients without a pathologic complete response to neoadjuvant therapy.

overall_design: MCF7 cells were growth in DMEM supplemented with 10% FBS up to 70% confluence and then transfected in OptiMEM using miR-18a mimic, antimiR-18a and controls for each condition (mimic or antimiR) in three biological replicates (6 well plates), 100 nM. After 48 hours, cells were lysed using RNAzol and total RNA was purified using Direct-zol™ RNA MiniPrep. After extraction, hybridization on Affymetrix microarrays was performed.

first: Elena

last: García-Martínez

first: Asunción

last: Chaves-Benito

first: Pablo

last: Conesa-Zamora

first: Esther

last: Navarro-Manzano

first: Enrique

last: González-Billalabeitia

first: Elisa

last: García-Garre

first: Alberto

last: Martínez-Carrasco

first: Vicente

last: Vicente

first: Francisco

last: Ayala de la Peña


title: Gene expression in Raw264.7 and THP-1 Cells following treatment with probiotics strains L. acidophilus, B. clausii and B. bifidum at MOI of 1 for 6 hrs: time-matched untreated cells vs. Probiotics-treated cells

first: Biswaranjan

last: Pradhan

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Gene expression kinetics in RAW 264.7 cells treated with Lactobacillus bulgaricus: Reference (Total RNA Mixture of all samples) vs. Probiotics treated cells

summary: Transcriptional profiling of RAW 264.7 cells on Lactobacillus bulgaricus treatment.

overall_design: Four conditions of the expriment, Untreated RAW 264.7 cells (NT) vs. treatment with Lactobacillus bulgaricus at MOI of 10 with 3 time points. Biological replicates: 3 in each case (Equal amount of total RNA from each replicate pulled together for microarray).

first: Pradhan

last: Biswaranjan

first: Guha

last: Dipanjan

first: Banerjee

last: Arka

first: Aich

last: Palok


title: Fast evolution of gained essential function by a young gene through gained interaction with other essential genes [RNA-Seq]

city: Irvine

first: Grace

last: Lee

institute: University of California, Irvine

overall_design: RNAseq of wildtypes and CRISPR-knock out mutant of CG7804

first: Manyuan

last: Long


title: Effect of IkBz (Nfkbiz) deficiency on oncogenic RAS transcriptional program

status: Public on May 29 2019

city: Bethesda

first: Christophe

last: Cataisson

state: Maryland

address: 37 Covent drive

institute: National Cancer Institute

summary:
The goal of the current study is to define the contribution of IkBzeta (Nfkbiz) to the transcriptional program ellicited by oncogenic v-RASHa in mouse primary keratinocytes
In this dataset we provide gene expression data from primary mouse keratinocytes in culture.

overall_design: 8 samples corresponding to 2 experimental conditions


title: Estrogen signaling is reprogrammed in breast tumorigenesis

city: Chicago

first: Hari

last: Singhal

state: IL

address: 929 E 57th St

department: Ben May Department for Cancer Research

institute: University of Chicago

summary:
Limited knowledge of the changes in estrogen receptor (ER) signaling during the transformation of the normal mammary gland to breast cancer hinders the development of effective prevention and treatment strategies. Differences in estrogen signaling between normal human primary breast epithelial cells and primary breast tumors obtained immediately following surgical excision were explored. Transcriptional profiling of normal ER+ mature luminal mammary epithelial cells and ER+ breast tumors revealed significant difference in the response to estrogen stimulation. Consistent with these differences in gene expression, the normal and tumor ER cistromes were distinct and sufficient to segregate normal breast tissues from breast tumors. The selective enrichment of the DNA binding motif GRHL2 in the breast cancer-specific ER cistrome suggests that it may play a role in the differential function of ER in breast cancer. Depletion of GRHL2 resulted in altered ER binding and differential transcriptional responses to estrogen stimulation. Furthermore, GRHL2 was demonstrated to be essential for estrogen-stimulated proliferation of ER+ breast cancer cells. DLC1 was also identified as an estrogen-induced tumor suppressor in the normal mammary gland with decreased expression in breast cancer. In clinical cohorts, loss of DLC1 and gain of GRHL2 expression are associated with breast cancer and are independently predictive for worse survival. This study suggests that normal ER signaling is lost and tumor-specific ER signaling is gained during breast tumorigenesis. Unraveling these changes in ER signaling during breast cancer progression should aid the development of more effective prevention strategies and targeted therapeutics.

SIGNIFICANCE STATEMENT:
Abnormal estrogen receptor (ER) signaling drives the majority of breast cancers and is targeted by endocrine therapies. However, in normal breast tissue, ER signaling has been demonstrated to promote benign functions such as development and differentiation. Using genomic techniques to characterize ER function in normal breast and breast tumors, this study reveals differential patterns of ER signaling, suggesting that normal ER signaling is lost and tumorigenic ER signaling gained during breast tumor formation. Better understanding of this process can aid the development of improved breast cancer prevention strategies and therapies.

overall_design: Methods: To model the normal breast epithelium, viable tissue specimens from patients undergoing reduction mammoplasty were obtained and enriched for breast epithelial cells via FACS. Fresh-frozen ER+ breast tumor samples were then obtained for comparison. RNA-seq, ChIP-seq for ER, and genome-wide CRISPR screening in the presence of estrogen stimulation were performed. These various modalities of genomic data were then integrated and analyzed to identify mechanistic patterns in breast tumorigenesis.

first: Myles

last: Brown


title: Apelin absence in endothelial cells

city: Vienna

first: Iris

last: Uribesalgo

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA

summary:
First, transcriptome analysis of purified CD31+ endothelial cells (ECs) from VEGF-treated sprouting embryoid bodies showed angiogenesis as the top affected category when Apelin is not present. In addition, loss of Apelin resulted in the modulation of pathways in ECs related to vasculogenesis, cell adhesion and response to hypoxia. Ingenuity Pathway Analysis (IPA) further identified VEGFR pathway as the main upstream regulator affected in endothelial cells, closely followed by the TGFβ1 and TNF pathways, all reduced in the absence of Apelin. The most inhibited genes from the VEGFR pathway in the absence of Apelin are angiogenesis-related genes.
Second, transcriptome analysis of CD31+/CD105+ ECs sorted from Apelin wild-type and Apln-depleted tumors found a significant decrease in processes associated with endothelial cell proliferation and angiogenesis in ECs sorted out of Apelin-depleted tumors using IPA. Further, IPA predicted a decrease in the adhesion of granulocytes and upstream regulator analysis showed that proteins of the TGF-superfamily, Inhibin-βA and TGF-β1, as well as C/EBP-alpha, β-Catenin, ErbB2 and EGFR are predicted to be inhibited upstream regulators in ECs isolated from Apelin-depleted tumors.

overall_design:
Transcriptome analysis of purified CD31+ endothelial cells from VEGF-treated in vitro sprouting vessels in Apelin presence or absence.

Transcriptome analysis of tumor endothelial cells from Apelin wild-type and depleted conditions. We report the application of Smart-Seq2 sequencing to populations of 100 endothelial cells, sorted from tumors that were Apelin wild-type or depleted.

first: Josef

last: Penninger

first: David

last: Hoffmann


title: Gene expression analysis of Influenza vaccine response in Young and Old - Year 5

status: Public on May 26 2019

city: New Haven

first: Hailong

last: Meng

state: CT

address: 300 George Str

institute: Yale University

summary: We profiled gene expression from a stratified cohort of subjects to define influenza vaccine response in Young and Old

overall_design:
Differential gene expression by human PBMCs from Healthy Adults receiving Influenza Vaccination (Fluvirin, Novartis). Healthy adults (older >65, younger 21-30 years) were recruited at seasonal Influenza Vaccination clinics organized by Yale University Health Services during October to December of 2014 – 2015 seasons. With informed consent, healthy individuals were recruited as per a protocol approved by Human Investigations Committee of the Yale University School of Medicine. Each subject was evaluated by a screening questionnaire determining self-reported demographic information, height, weight, medications and comorbid conditions. Participants with acute illness two weeks prior to vaccination were excluded from study. Blood samples were collected into BD Vacutainer Sodium Heparin tube at four different time points, once prior to administration of vaccine and three time points after vaccination on days 2, 7 and 28. Peripheral Blood Mononuclear Cells (PBMC) were isolated from heparinized blood using Histopaque 1077 in gradient centrifugation. About 1.0x10^7 freshly isolated PBMC were lysed in Triso and immediately stored in -800C. Total RNA in aqueous phase of Trisol - Chloroform was isolated in an automated QiaCube instrument using miRNeasy according to manufacturer’s instructions. Integrity of RNA samples were assessed by Agilent 2100 BioAnalyser Samples were processed for cRNA generation using Illumina TotalPrep cRNA Amplification Kit and subsequently hybridized to Human HT12-V4.0 BeadChip at Yale Center for Genomic Analysis (YGCA).

The current data set, together with GSE59654, GSE59635, GSE59743, and GSE101709, represents subsets of the same overall study

first: Albert

last: Shaw

first: Subhasis

last: Mohanty

first: Steven

last: Kleinstein

first: Sui

last: Tsang

first: Stefan

last: Avey


title: Fast evolution of gained essential function by a young gene through gained interaction with other essential genes

state: CA


title: Expression data from B cells expressing human AIRE

status: Public on May 25 2019

city: Tokushima

first: Mitsuru

last: Matsumoto

address: 3-18-15 Kuramoto

department: Division of Molecular Immunology

institute: Institute for Enzyme Research, Tokushima University

summary: Aire in medullary thymic epithelial cells plays an essential role in the establishment of self-tolerance through expression of broad arrays of tissue-restricted antigens. We asked what would happen if human AIRE is additively expressed in antigen-presenting cells in the thymus and periphery.

overall_design: We established a human AIRE-transgenic mouse line on NOD-background using MHC class II promoter and hybridization was performed on Affymetrix microarrays.

first: Hitoshi

last: Nishijima


title: Sequencing Facilitates Quantitative Analysis of gene expression among 3 stromal cell populations: NAF, CAF, CAF_HiP

city: Los Angeles

first: Neil

middle: A.

last: Bhowmick

state: California

address: 8750 Beverly Blvd., Atrium Building Room#103

department: Hematology/Oncology

institute: Cedars Sinai Medical Center

summary:
Purpose : Primary cultured fibroblast cultures can be classified based on their tumor promoting ability. Normal associated fibroblasts (NAF) cannot transform benign epithelia. Cancer associated fibroblasts  (CAF) can transform benign epithelia into cancer. As described in Kato and Placencio et al., High passage CAF (CAF_HiP) cells have lost the ability to potentiate tumor growth. This study sought to identify the differences among three groups of fibroblasts: NAF, CAF, and CAF_HiP
Methods :Human male prostatectomy tissues were cultured to generate primary cultured fibroblast cultures.
Results and Conclusions : Differential gene expression among the top 200 genes analzed as described in Kato and Placencio et al. revealed 33 secreted proteins. SFRP1 was confirmed to be highly expressed in CAF and was shown to play a role in prostate cancer tumor progression and neuroendocrine differentiation.

overall_design: Fibroblasts mRNA profiles were generated for NAF, CAF, and CAF_HiP using Ion Proton sequencer (Life technologies)

first: Manabu

last: Kato


title: KDM4B epigenetically protects against obesity and metabolic dysfunction

status: Public on May 22 2019

first: Cunyu

last: Wang

address: 10833 Le Conte Ave

department: School of Dentistry

institute: university of California, Los Angeles


title: KDM4B epigenetically protects against obesity and metabolic dysfunction [ChIP-seq]

summary: Preadiocyte of Kdm4b KO mice was infected with control or Flag-KDM4B retrovirus and were differentiated to adipocyte. The well-differentiated adipocytes were harvested for ChIP-Seq with Flag antibody.

overall_design: Identification of genome-wide binding sites of KDM4B


title: KDM4B epigenetically protects against obesity and metabolic dysfunction [gene expression]

summary:
KDM4B (lysine demethylase 4B) in adipose tissues plays a critical role in energy balance, oxidation, lipolysis and thermogenesis. Loss of KDM4B in mice resulted in obesity associated with reduced energy expenditure and impaired adaptive thermogenesis.
Mechanistically, we determined that KDM4B directly controls the expression of multiple metabolic genes.

overall_design: To explore the molecular mechanisms of Kdm4b deficiency-induced obesity, we performed a microarray analysis on the Epi, SubQ and BAT of 2-month-old WT and whole body Kdm4b KO mice

first: Yingduan

last: Cheng


title: Mnase-Seq study of Arabidopsis thaliana mutant chr5

status: Public on May 23 2019

city: Ithaca

first: Jian

last: Hua

address: 158 Emerson Hall

department: Plant Biology

institute: Cornell University

summary: Comparative study of nuclesome occupancy in Arabidopsis thaliana mutant chr5 and wild type strain.

overall_design: Mnase digest of chromatin from wt and chr5 mutants, library construction of protected DNA, Illumina Sequencing

first: Baohong

last: Zou

first: Qi

last: Sun

first: Wenli

last: Zhang


title: SmcHD1 genome-wide occupancy

city: Burnaby

first: Shabnam

last: Massah

state: British Columbia

address: 8888 University Drive

institute: Simon Fraser University

summary: To identify SmcHD1 genome-wide occupancy relative to global level of DNA methylation, we generated anti-SmcHD1 antiserum and used it in chromatin immunoprecipitation assay. We used SH-SY5Y neurobalstoma cells treated with DNA demethylating agent 5azaC for 72 hours to induce global loss of DNA methylation. The protein level of maintenance DNA methyltransferase dnmt1 was significatly reduced upon 5azaC treatment. The 5azaC treated and non-treated cells were then used for chromatin immunoprecipitation.

overall_design: Examination of SmcHD1 genome occupancy in SH-SY5Y cells treated with 5azaC compared with non-treated cells

first: Gratien

last: Prefontaine


title: Early response to loss of Argonaute proteins in embryonic stem cells activates the Tgf-ß/Smad Transcriptional Network

first: Jesse

last: Zamudio

institute: University of California, Los Angeles

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

overall_design: Refer to individual Series


title: Notch2 in mesenchymal stromal cells regulates canonical Wnt signalling in CLL cells

status: Public on May 20 2019

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

summary: We used microarrays to investigate differential gene expression in mouse bone marrow derived mesenchymal stromal cells, proficient or deficient for Notch2, cultured for 5 days in the presence or absence with primary CLL cells from 6 patients

overall_design: Notch2 pro- and deficient MSCs were co-cultured with 6 individual primary CLLs

first: I

last: Ringshausen

first: L