title: Inhalation of Lung Spheroid Cell-Secreted Factors and Exosomes Promotes Therapeutic Lung Repair in Rodent Models of Pulmonary Fibrosis

status: Public on Nov 18 2019

first: Xinxia

last: Peng

summary: Idiopathic pulmonary fibrosis (IPF) is a fatal form of interstitial lung disease in which persistent injury results in scar tissue formation. As fibrosis thickens, the lung tissue becomes stiff and losses the ability to facilitate gas exchange and provide cells with needed oxygen. Currently, IPF has few treatment options and no effective therapies, aside from lung transplant. Here we present a series of studies utilizing lung spheroid cell-derived conditioned media (LSC-CM) and exosomes (LSC-EXO) to treat different rodent models of lung injury and fibrosis. Inhalation treatment was given for seven consecutive days via a nebulizer for clinical relevance. Results revealed that LSC-CM and LSC-EXO treatments could attenuate and resolve bleomycin- and silica-induced fibrosis by reestablishing normal alveolar structure, decreasing collagen accumulation, and myofibroblast proliferation. In addition, LSC-CM and LSC-EXOs exhibited superior therapeutic benefits than their counterparts derived from bone marrow mesenchymal stem cells. LSC-CM and LSC-EXOs provide promising therapeutic options for pulmonary fibrosis.

overall_design: Exosomes were collected and purified from human lung spheroid cells (LSCs) and mesenchymal stem cells (MSCs) and their small RNAs were sequenced on a Nextseq500 sequencer (Illumina) using 45bp single-end reads.

first: Phuong-Uyen

last: Dinh

first: Dipti

last: Paudel

first: Hayden

last: Brochu

first: Jhon

last: Cores

first: Ke

last: Huang

first: M

last: Hensley

first: Erin

first: Adam

last: Vandergriff

first: Raina

last: Barrio

first: Tyler

last: Allen

first: Kevin

last: Blackburn

first: Thomas

last: Caranasos

first: Lauren

middle: V

last: Schnabel

first: Kenneth

middle: B

last: Adler

first: Leonard

last: Lobo

first: Michael

last: Goshe

last: Cheng


title: KLF4 binding is involved in the organization and regulation of 3D enhancer networks during acquisition and maintenance of pluripotency [RNA-seq]

status: Public on Sep 06 2019

city: New York

first: Effie

last: Apostolou

state: NY

address: 1161 York Avenue, Apt 8A

country: USA

institute: Weill Cornell Medicine

type: Expression profiling by high throughput sequencing

summary: Cell fate transitions are accompanied by global transcriptional, epigenetic and topological changes driven by transcription factors (TFs), as is strikingly exemplified in somatic cell reprogramming to pluripotent stem cells (PSCs) by OCT4, KLF4, SOX2 and cMYC. How TFs orchestrate the complex molecular changes around their targets in a temporal manner remains largely elusive. Here, using KLF4 as a paradigm, we provide the first TF-centric view of chromatin reorganization and the association to 3D enhancer rewiring and the transcriptional changes of linked genes during reprogramming of mouse embryonic fibroblasts to (MEFs) to PSCs. Inducible depletion of KLF factors in PSC caused a genome-wide decrease in connectivity of enhancers and disruption of KLF4 binding site from PSC-specific enhancers was sufficient to reduce expression of genes within the enhancer hub partly by impairing long-range contacts. Our study provides an integrative view of the intricate activities of a master regulator during a controlled cell fate transition and offers novel insights into the order and nature of molecular events that follow TF binding.

overall_design:
Integrative analysis of ChIP-seq, HiChIP, HiC, ATAC-seq, RNA-seq and 4C-seq techniques.
RNA-seq TKO samples: RNA-seq was performed in 2 WT ESC cell populations and 2 ESC cell populations after KLF KO. RNA was extracted from 2 biological replicates at 0 hours (WT cells) and 24 hours after KLF KO.

first: E


title: KLF4 binding is involved in the organization and regulation of 3D enhancer networks during acquisition and maintenance of pluripotency [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Summary: Cell fate transitions are accompanied by global transcriptional, epigenetic and topological changes driven by transcription factors (TFs), as is strikingly exemplified in somatic cell reprogramming to pluripotent stem cells (PSCs) by OCT4, KLF4, SOX2 and cMYC. How TFs orchestrate the complex molecular changes around their targets in a temporal manner remains largely elusive. Here, using KLF4 as a paradigm, we provide the first TF-centric view of chromatin reorganization and the association to 3D enhancer rewiring and the transcriptional changes of linked genes during reprogramming of mouse embryonic fibroblasts to (MEFs) to PSCs. Inducible depletion of KLF factors in PSC caused a genome-wide decrease in connectivity of enhancers and disruption of KLF4 binding site from PSC-specific enhancers was sufficient to reduce expression of genes within the enhancer hub partly by impairing long-range contacts. Our study provides an integrative view of the intricate activities of a master regulator during a controlled cell fate transition and offers novel insights into the order and nature of molecular events that follow TF binding.

Purpose: We captured on a genome-wide scale the binding of KLF4 during iPSC formation and its effects on chromatin state, transcriptional activity and chromatin topology around its targets.

Methods: We used a well-characterized reprogramming system to apply genome-wide assays that map KLF4 binding (ChIP-seq), chromatin accessibility (ATAC-seq), enhancer and gene activity (H3K27ac ChIP-seq and RNA-seq), enhancer connectivity (H3K27ac Hi-ChIP) as well as KLF4-centric chromatin looping (KLF4 Hi-ChIP) at different stages during acquisition of pluripotency.

Results: Integrative analysis of our results generated a reference map of stage-specific chromatin changes around KLF4 bound loci and established strong links with enhancer. rewiring and concordant transcriptional changes. Genetic manipulation of KLF4 binding from a PSC enhancer further supported the ability of KLF4 to function both as a transcriptional regulator and a chromatin organizer.

Conclusions: Our study offers novel insights into the intricate roles of a master regulator during cell fate transition.

overall_design: Mouse embryonic fibroblasts (MEFs) (Rosa26-M2rtTA/Col1a1-OKSM) induced with doxycycline (dox) in the presence of ascorbic acid. We collected bulk populations on day 3 after dox treatment, whereas at later stages, on day 6 and day 9, we sorted SSEA1 positive cells to enrich for cells on the trajectory towards induced pluripotency. Finally, we used pluripotent stem cells (PSCs) inclusive of embryonic stem cells (ESCs) as a reference point for established pluripotency. Biological replicates were collected to assay for chromatin accessibility (paired-end ATAC-seq), gene activity (single-end RNA-seq), H3K27ac ChIP-seq (single-end) in MEFs, day3, 6, 9 and PSCs. KLF4 binding (single-end ChIP-seq) was assessed in day3, 6, 9 and PSCs. KLF4/H3K27ac centric looping (paired-end Hi-ChIP) was studied in either day3, day6 and PSCs for KLF4 or MEFs and PSCs for H3K27ac.

first: Aristotelis

last: Tsirigos


title: KLF4 binding is involved in the organization and regulation of 3D enhancer networks during acquisition and maintenance of pluripotency [ATAC-seq]


title: Circulating tumor cells exit circulation while maintaining multicellularity augmenting metastatic potential

status: Public on Aug 26 2019

city: Raleigh

first: Xinxia

last: Peng

address: 1060 William Moore Drive

institute: North Carolina State University

summary: Metastasis accounts for the majority of all cancer deaths, yet the process remains poorly understood. A pivotal step in the metastasis process is the exiting of tumor cells from the circulation, a process known as extravasation. However, it is unclear how tumor cells extravasate, and if multicellular clusters of tumor cells posses the ability to exit as a whole or must first disassociate. In this study, we use in vivo zebrafish and mouse models to elucidate the mechanism tumor cells use to extravasate. We found that circulating tumor cells exit the circulation using the recently identified extravasation mechanism, angiopellosis, and do as both clusters and individual cells. We further show that when melanoma and cervical cancer cells utilize this extravasation method to exit as clusters, they exhibit an increased ability to form tumor at distant sites through the expression of unique genetic profiles. Collectively, we present a new model for tumor cell extravasation of both individual and multicellular circulating tumor cells.

overall_design: Mouse B16 cells infused into zebrafish, but which did not participate in extravasation represent control samples.

middle: A

first: Jeffrey

last: AYoder


title: The effect of knockdown of SUN1/2 on LPS-primed macrophages

status: Public on Sep 01 2019

city: Shanghai

first: Shi

last: Jiao

address: 320 Yue Yang Road

country: China

institute: Shanghai Institutes of Biological Sciences

summary: SUN1/2 are located on the inner nuclear envelope membrane, which comprise an N-terminal nucleoplasmic domain, a transmembrane segment and a C-terminal SUN domain. The nucleoplasmic domain of SUN1/2 interacts with lamina and/or chromatin binding proteins, while the SUN domain protrudes into the lumen of the nuclear envelope to interact with KASH proteins in a trimeric fashion. Defects in SUN proteins have been linked to human diseases including laminopathies, ataxia, progeria, lissencephaly, and cancer. To explore the role of SUN1/2 during macrophage activation, we explore microarray analysis of THP-1-derived macrophages after stable transfection of siVGLL4 for 48 h.

overall_design: nc-1, nc-2, siSUN1/2-1, siSUN1/2-2 in THP-1 cells

first: Zhaocai

last: Zhou


title: KLF4 binding is involved in the organization and regulation of 3D enhancer networks during acquisition and maintenance of pluripotency [HiChIP and HiC]


title: Chemically Induced CD24+ hepatocyte-derived liver progenitor-like cells revert chronic hepatic dysfunction

status: Public on Jul 01 2019

city: shanghai

first: yan

last: hexin

address: No. 1630 East Road

institute: Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine

summary: Administration of soluble molecules to induce endogenous adult liver progenitor-like cells may provide a clinically and effectively applicable approach for liver damage repair. Here, we report that HGF in combination with a cocktail of small molecules Y-27632, A-83-01, and CHIR99021 (HACY), which we have previously defined to convert mature hepatocytes (MHs) to liver progenitor-like cells (HepLPCs) in vitro, could induce the replenishment of endogenous HepLPCs and relieve chronic liver dysfunction during persistent injury. The liver progenitor cells surface marker, CD24, was found to be highly expressed in HepLPCs in vitro. Similarly, injection of HACY into mice with carbon tetrachloride (CCL4) treatment also induced conversion of mature hepatocytes to CD24+ progenitor-like cells in vivo, leading to the attenuation of liver fibrosis. Compared to the liver progenitor cells (LPCs) derived from nonparenchymal cells, HACY-induced CD24+ HepLPCs retained an increased hepatic function by RNA sequencing analysis and could promote restoration of liver function by replacing CCL4-impaired liver cells during chronic hepatic damages. And CD24+ liver stem cells could also be observed in human liver fibrosis tissues and expanded in 3D hepatic spheroid in the present of HACY. Together, the results of our study indicated that injection of a cocktail of HACY might be a valuable multiple targets therapy for patients with chronic liver fibrotic pathologies.

overall_design: global expression analysis of RNA sequencing data to compare expression levels of MACS-sorted CD24+ cells from CCL4 and HACY treatment

first: Huang

last: Weijian

first: Yan

last: Hexin


title: Maternal obesity has sex dependent effects on liver transcriptome in young adult rat offspring

status: Public on Jun 25 2019

city: Mexico

first: CONSUELO

last: LOMAS

state: MEXICO

address: Vasco de Quiroga 15, Belisario Domínguez Sección XVI,

department: REPRODUCTIVE BIOLOGY

country: Mexico

institute: INCMNSZ

summary:
Maternal high-fat diet consumption predisposes to metabolic and liver dysfunction in F1 male and female at young adulthood.
Purpose:  We used RNA-seq to determine the liver transcriptome of male and female F1 of MO and control fed mothers.
Methods: Female Wistar rat mothers ate control (C) or obesogenic (MO) diet from the time they were weaned through breeding at postnatal day (PND) 120, delivery and lactation. After weaning all male and female F1 ate control diet. At PND 110  liver and fat were collected to analyze metabolites, histology and liver differentially expressed genes. To identify the functional F1 liver changes due to MO, we evaluated the differentially expressed genes (DEGs) between MO and C males and females with separate pairwise comparisons due to the marked differences between males and females. Genes were filtered based on ≥ 1.4 fold change (FC) and nominal P value <0.05 (Student´s t-test).
Results: MOF1 males presented greater physiologic and histological NAFLD characteristics than MOF1 females. RNA-seq revealed 1,365 genes significantly changed in male MOF1 liver and only 70 genes in MOF1 female compared with controls. GO and KEGG analysis identified differentially expressed genes related to metabolic process. Male MOF1 liver showed the following altered pathways: insulin signaling (22 genes), phospholipase D signaling (14 genes), NAFLD (13 genes), and glycolysis/ gluconeogenesis (7 genes). In contrast, few genes were altered in these pathways in MOF1 females.
Conclusions: These results improve understanding of the mechanism by which a maternal high fat diet affects their F1. In summary, MO programs sex-dependent F1 changes in insulin, glucose and lipid signaling pathways, leading to liver dysfunction and insulin resistance. Male adult MOF1 livers show global down-regulation of genes that are required for normal function of major liver metabolic pathways. This new knowledge is important for producing sex-specific interventions.

overall_design: Liver transcriptomic profiles from young male and female adult rat offspring of control and obese mothers  were analyzed by RNA-seq. 22 samples, 5-6 animals per group: 1) Control MALE n=6, 2) MO MALE,n=5 3) Control FEMALE, n=6  and 4) MO FEMALE n=5.

first: Consuelo

last: Lomas-Soria

first: Peter

middle: W

last: Nathanielsz

first: Laura

last: Cox

first: Elena

last: Zambrano


title: KLF4 binding is involved in the organization and regulation of 3D enhancer networks during acquisition and maintenance of pluripotency

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

overall_design: Refer to individual Series


title: Transcriptome-wide dynamics of extensive m6A mRNA methylation during Plasmodium falciparum blood-stage development

status: Public on Jun 18 2019

city: Paris

first: Sebastian

last: Baumgarten

address: 25, Rue du Dr. Roux

department: Parasites and Insect Vectors

country: France

institute: Institut Pasteur

summary: Malaria pathogenesis results from the asexual replication of Plasmodium falciparum within human red blood cells, which relies on a precisely timed cascade of gene expression over a 48-hour life cycle. However, post-transcriptional control of this hardwired program has been largely unexplored. To this end, we performed a comprehensive characterization of m6A mRNA methylation during the different developmental stages. Using mass spectrometry and parallel m6A and RNA sequencing, we show that m6A is developmentally regulated and present at higher levels (>4-fold) than in other organisms investigated. Knockdown of the m6A methyltransferase by CRISPR interference leads to increased levels of transcripts that normally contain m6A. In accordance, we find an inverse correlation between m6A status and mRNA half-life or translational efficiency. Our data demonstrate the crucial function of extensive m6A mRNA methylation in dynamically fine-tuning the transcriptional program of a unicellular eukaryote and reveal a new ‘epitranscriptomic’ layer of gene regulation in malaria parasites.

overall_design: Characterization of m6A mRNA methylation dynamics during Plasmodium falciparum blood stage development. The m6A methyltransferase was knocked out using CRISRP interference and the dCas9 binding site was identified by dCas9 ChIP-seq. m6A-seq was performed in two replicates of the knock-down (gPfMT-A70 ) and control (gControl) parasite cell line at 12, 24  and 36 hours post infection (hpi). BioProject accession: PRJNA473770

first: Jessica

middle: M

last: Bryant

first: Artur

last: Scherf


title: The p30 isoform of CEBPA uncovers a silent enhancer to drive the expression of the tumor promotive factor CD73 in CEBPA mutant AML

status: Public on Jul 30 2019

city: Copenhagen N

first: Janus

middle: Schou

last: Jakobsen

address: Ole Maaløes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

summary: CEBPA is a key hematopoietic transcription factor (TF), found mutated in 5-14% of all acute myeloid leukemia (AML) cases, but the direct molecular ramifications of this driver mutation remains elusive. To investigate CEBPA-mutant AML, we compared patient aberrant genetic programs with changes in a precise mouse model (Lp30) expressing only the cancer-prevalent truncated CEBPA, p30, and identified a stringent cross-species AML program. Small-scale ChIP-seq methodology revealed aberrantly activated enhancers, exclusively occupied by CEBPA in leukemia. One cancer-enhancer upstream of Nt5e, encoding CD73, was physically and functionally linked to this conserved AML gene, and could be activated by CEBPA. Targeting of CD73-adenosine signaling increased survival in AML transplanted mice. Our data thus indicate a first-in-class link between a TF cancer driver mutation and a druggable, direct transcriptional target.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq of samples of human healthy donors vs CEBPA-biallelic AML patients was compared to RNA-seq of mouse WT versus CEBPA-biallelic AML model Lp30. ChIP-seq of CEBPA, Histone marks H3K27ac and H3K4me1 in mouse WT versus CEBPA-biallelic AML model Lp30. ChIP-seq of histone mark H3K27ac in samples of human healthy donors versus mono-allelic and biallelic CEBPA-mut AML. All samples are rigorously FACS isolated GMP phenotypic cells, in vivo material. RNA-seq, different shRNA constructs, Nt5e-KD versus scramble-KD in mouse Lp30 CEBPA-biallelic model cells in tissue culture.

middle: S

first: Linea

middle: G

last: Laursen

first: Mikkel

last: Schuster

first: Sachin

last: Pundhir

first: Nicolas

last: Rapin

first: Erwin

last: Schoof

first: Ying

last: Ge

first: Kristoffer

last: Vitting-Seerup

first: Coline

last: Gentil

first: Johan

last: Jendholm

last: Hokland

first: Jude

last: Fitzgibbon

first: Bo

middle: T

last: Porse


title: Quantitative multiplexed ChIP-Seq (MINUTE-ChIP) Calibration Experiment

status: Public on Jun 21 2019

city: Solna

first: Simon

middle: J

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: In MINUTE-ChIP, native chromatin is fragmented using Micrococcal nuclease, and subsequently blunted and ligated to double-stranded DNA adaptors that include a T7 RNA polymerase promoter and a sample barcode sequence. Finally, samples are combined and subsequent ChIP reactions are performed with the pooled samples. ChIP material is prepared into an Illumina-compatible library using linear amplification by virtue of T7 RNA polymerase, reverse transcription and a low-cycle library PCR amplification.  Native MINUTE-ChIP is based on Mint-ChIP, developed by the Bernstein lab (van Galen et al., 2016; PMID: 26687680). We have introduce unique molecule (UMI) counting and paired-end mapping of the chromatin fragments to this method, which we then termed MINUTE-ChIP for multiplexed indexed unique molecule T7 amplification end-to-end sequencing. Here, we generate a standard curve for H3K27me3 and demonstrate that MINUTE-ChIP has a large linear dynamic range, thus MINUTE-ChIP quantitation is proportional to real quantities.

overall_design: We treated mESC either with EZH2 inhibitor EPZ-6438 to reduce H3K27me3 below detectable levels, or with an inhibitor to demethylases JMJD3/UTX, GSK-J4, to increase H3K27me3 above physiologic levels. Mixing cells from these two treatments, H3K27me3 low (L) and H3K27me3 (H), in defined ratios (100:0, 95:5, 75:25, 50:50, 25:75 5:95, 0:100 L:H), we created an artificial gradient of H3K27me3. Two replicates were prepared from each mixing ratio using two different barcodes and pooled for MINUTE-ChIP. From this pool, ChIP was performed in parallel using H3K27me3, H3K27me2, H3K27me1 and H3 antibodies. After demultiplexing reads by barcode and UMI-deduplication, reads were mapped to the mm9 genome. Total mapped read counts per barcode were normalized to the respective input read counts, essentially correcting for uneven barcode representation in the input. The resulting Input Normalized Mapped Read Count (INRC) is a quantitative, proportional measure of the abundance of ChIP epitope, e.g. H3K27me3, for each barcode.

last: Elsasser

first: Banushree

last: Kumar


title: Ribosome queuing enables non-AUG translation to be resistant to multiple protein synthesis inhibitors

status: Public on Jun 05 2019

city: Baltimore

first: Daniel

last: Goldman

state: Maryland

address: 725 N. Wolfe St.

department: Molecular Biology and Genetics

institute: Johns Hopkins School of Medicine

summary: Aberrant translation initiation at non-AUG start codons is associated with multiple cancers and neurodegenerative diseases. Nevertheless, how non-AUG translation is regulated differently from canonical translation is poorly understood. We thus used start codon-selective  reporters and ribosome profiling to characterize how translation from non-AUG start codons responds to protein synthesis inhibitors in human cells. These analyses surprisingly revealed that translation of non-AUG reporters and the endogenous GUG-encoded DAP5 (eIF4G2/p97) mRNA are resistant to cycloheximide (CHX), a translation inhibitor which slows but does not completely abrogate elongation. Our data suggest that slowly elongating ribosomes cause queuing of scanning pre-initiation complexes (PIC), preferentially enhancing otherwise poor recognition of non-AUG start codons. Consistent with this model, limiting PIC formation or scanning sensitizes non-AUG translation to CHX. Moreover, PIC queuing can cause translation from an AUG codon in a poor context to become less sensitive to CHX. We further find that non-AUG translation is resistant to other inhibitors that target ribosomes within the coding sequence, but not those targeting newly initiated ribosomes. In total, these data indicate that ribosome queuing enables mRNAs with poor initiation context, namely those from non-AUG start codons, to be resistant to pharmacological inhibitors.

overall_design: Measuring translational efficiency genome-wide in response to prolonged cyclohexamide treatment

first: Michael

last: Kearse

first: Jiou

last: Choi

first: Chike

last: Nwaezeapu

first: Dongming

last: Liang

first: Katelyn

last: Green

first: Aaron

last: Goldstrohm

first: Peter

last: Todd

first: Rachel

first: Jeremy

last: Wilusz


title: Epigenetic activation and memory at a TGFB2 enhancer in systemic sclerosis

status: Public on May 21 2019

first: Joseph

middle: Y

last: Shin

state: MD

address: 733 N Broadway MRB-539

institute: Johns Hopkins University School of Medicine

summary: Epigenetic activation of an enhancer for TGFB2 locks SSc patient fibroblasts into a pro-fibrotic synthetic state through mechanisms dependent on NF-kB and BRD4.

overall_design: Examination of chromatin accessibility and transcriptome of healthy control and patient fibroblasts

first: Harry

middle: C

last: Dietz


title: PTEN interacts with the transcription machinery on chromatin and regulates RNA polymerase II-mediated transcription [Affymetrix]

status: Public on Apr 03 2019

first: Ramon

last: Parsons

address: 1425 Madison Avenue

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: We demonstrate that PTEN interacts with the transcription machinery. Using ChIP-seq, we show that PTEN co-localizes with RNAPII and binds to chromatin in promoter and putative enhancer regions. We further show that loss of PTEN affects RNAPII occupancy in gene bodies and correlates with gene expression changes. Loss of PTEN also increased cells’ sensitivity to transcription inhibition via small molecules.

overall_design: We interogateMEF cell lines for transcriptional changes after Pten loss and correlate those with changes in RNAPII occupancy at promoters, regulatory regions and in gene bodies.

first: Nicole

last: Steinbach

first: Elias

middle: E

last: Stratikopoulos

first: Emily

last: Bernstein


title: PTEN interacts with the transcription machinery on chromatin and regulates RNA polymerase II-mediated transcription


title: Whole transcriptome profiling of bast fibers of ramie

status: Public on May 02 2019

city: Changsha

first: Touming

last: Liu

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

type: Non-coding RNA profiling by high throughput sequencing

summary: Ramie fibers extracted from the stem barks have been utilized for thousands years in China, and its biosynthetic mechanism is poorly understood. Here, we have characterized and compared the expression profiling of the barks from the top and middle part of stem where the secondary cellular walls (SCWs) of fiber cell have not initiated growth and was thickening, respectively; resulting in 4,520 differential expression (DE) protein-coding transcripts (PCTs), 1,287 DE long noncoding RNAs (lncRNAs), 88 DE miRNAs and 78 DE circular RNAs (circRNAs). Among the 4,520 DE PCTs, 75 were identified to be the homolog of the Arabidopsis SCW-biosynthetic genes. Overexpression of whole_GLEAN_10014861 (a homolog of SND1) in Arabidopsis caused a significant up-regulation in the expression of AtMYB46 and AtMYB83 that are two key regulators for SCW biosynthesis, thus conferring more fiber cells, along with a remarkable thickening in the SCWs of these cells. Bioinformatic prediction revealed 14 of the 75 homolog targeted by 16 noncoding RNAs (including 8 miRNAs and 8 lncRNAs), and two involved in the competing endogenous RNAs networks, indicating a complex regulatory network for the SCW biosynthesis of bast fiber in ramie. This study provides important insights into the bast fiber biosynthesis of ramie.

overall_design:
Experimental material, tissue sampling and RNA isolation: Elite cultivar Zhongzhu 1 was planted in the experimental farm of the Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Yuanjiang, China in June 2016. The TPS and MPS barks were separately collected from five individuals of Zhongzhu 1, immediately frozen in liquid nitrogen. Three replicates were sampled for TPS and MPS barks, respectively. Total RNA of this sample was extracted using an E.Z.N.A. Plant RNA Kit (OMEGA Bio-Tek, Norcross, GA, USA) according to the manufacturer’s protocol.
Libraries construction and sequencing: Total RNAs from six samples were used separately to construct the small RNAs, circRNAs and cDNA libraries, respectively. The small RNAs sequencing was performed using BGISEQ-500 platform (BGI, Shenzhen, China), and circRNAs and transcriptome were sequenced using the Illumina sequencing platform (HiSeq™ 2500; Illumina, San Diego, CA), according to the manufacturer's instructions of corresponding platform. Thereafter, the raw reads for each sample were filtered, generating clean reads used in next analysis.


title: Tabula Muris Senis: Bulk sequencing

status: Public on Jun 17 2019

city: San Francisco

first: Angela

last: Oliveira Pisco

state: CA

address: 499 Illinois St

department: Data Science

institute: Chan Zuckerberg Biohub

summary: Bulk RNA sequencing of 17 organs from Mus musculus across the organism's life span.

overall_design: This dataset contains the transcriptomic information of 17 organs from Mus musculus across the organism's life span.

first: Nick

last: Schaum

first: Shayan

last: Hosseinzadeh

first: Oliver

last: Hahn

middle: O

last: Pisco

first: Spyros

last: Darmanis

first: Tony

last: Wyss-Corray

first: Stephen

middle: R

last: Quake


title: Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments

status: Public on Mar 18 2019

first: Christopher

last: Jackson

address: 101 Avenue of the Americas

department: Center for the Genomics of Neurodegenerative Disease

institute: New York Genome Center

summary: Understanding how gene expression programs are controlled requires identifying regulatory relationships between transcription factors and target genes. Gene regulatory networks are typically constructed from gene expression data acquired following genetic perturbation or environmental stimulus. Single-cell RNA sequencing (scRNAseq) captures the gene expression state of thousands of individual cells in a single experiment, offering advantages in combinatorial experimental design, large numbers of independent measurements, and accessing the interaction between the cell cycle and environmental responses that is hidden by population-level analysis of gene expression. To leverage these advantages, we developed a method for transcriptionally barcoding gene deletion mutants and performing scRNAseq in budding yeast (Saccharomyces cerevisiae). We pooled diverse genotypes in 11 different environmental conditions and determined their expression state by sequencing 38,285 individual cells. We developed, and benchmarked, a framework for learning gene regulatory networks from scRNAseq data that incorporates multitask learning and constructed a global gene regulatory network comprising 11,866 interactions.

overall_design: 12 yeast genotypes, consisting of a wild-type control and 11 transcription factor deletions, with 6 unique biological replicates for each genotype, totaling 72 uniquely barcoded strains. All strains are pooled, grown in various culture conditions, library prepped with the 10x genomics chromium 3' system, and sequenced. An additional control experiment using bulk TRIZOL-extracted RNA is included.

first: David

last: Gresham

first: Richard

last: Bonneau


title: Simultaneous profiling of sexually transmitted bacterial pathogens, microbiome, and concordant host response in cervical samples using whole transcriptome sequencing analysis

status: Public on Mar 19 2019

first: Xinxia

last: Peng

summary: We examined the potential for characterization of host, pathogen and microbiome interactions at a molecular level and identification of novel, outcome-relevant biomarkers in a single, easily obtained, clinical specimen using total RNA-seq.

overall_design:
Examination of human cervical swabs via total RNA-seq
CT = Chlamydia trachomatis
GC = Neisseria gonorrhoeae
MG = Mycoplasma genitalium
TV = Trichomonas vaginalis

first: Catherine

last: O'Connell

first: Hayden

last: Brochu

first: Jenna

last: Girardi

first: Erin

last: Harrell

first: Aiden

last: Jones

first: Toni

last: Darville

first: Arlene

last: Seña-Soberano


title: PTEN interacts with the transcription machinery on chromatin and regulates RNA polymerase II-mediated transcription.[RNA-seq and ChIP-seq]

first: Ramon

last: Parsons

overall_design: We interogate HeLa, MEF and MycOE mouse breast tumor cell lines for transcriptional changes after PTEN loss and correlate those with changes in PTEN, RNAPII, RNAPII Ser2P, RNAPII Ser5P occupancy at promoters, regulatory regions and in gene bodies.

first: Nicole

last: Steinbach

first: Dan

last: Hasson

first: Ravi

last: Sachidanandam

first: Emily

last: Bernstein


title: Inhibition of DOT1L and PRMT5 promote synergistic anti-tumor activity in a human MLL leukemia model induced by CRISPR/Cas9

status: Public on Mar 16 2019

city: Tuebingen

first: Corina

last: Schneidawind

address: Otfried-Mueller-Str. 10

department: Hematology and Oncology

country: Germany

institute: University Hospital Tuebingen

summary: Previous studies have identified frequent MLL-AF4 chromosomal translocation breakpoints in patients. Using CRISPRscan, we designed different sgRNAs recognizing patient-specific sequences in intron 11 of the MLL and exon 3 of the AF4 genes, respectively. Using plasmid- and virus-free delivery of sgRNAs with Cas9 protein, we nucleofected CD34+ target cells derived from human umbilical cord blood. Following nucleofection, the cells were maintained in liquid culture supplemented with cytokines and chemokines optimized for growth of MLLr cells. On day 30 (MLL-AF4)  of liquid culture,  MLL translocations were detcted in 100% of cells by FISH analysis allowing for further analysis of pure MLLr cells. MLL-AF4 translocated cells and the respective control cells from the two different donors were maintained in similar culture conditions. After reaching 100% purity of the MLLr cells, they were subjected to RNA-seq.

overall_design: huCB CD34+ cells were engineered to bear endogenous MLL-AF4 translocations. RNA sequencing was performed using TruSeq mRNA Stranded Sequencing (Illumina) of two donors comparing engineered and non-treated cells, respectively.

first: Kathy-Ann

last: Secker


title: Fisetin induces autophagy in pancreatic cancer cells via endoplasmic reticulum stress- and mitochondrial stress-dependent pathways

status: Public on Feb 25 2019

city: Hangzhou

first: Xiao

middle: Dong

last: Xu

state: Zhejiang province

address: Administrative Building,3 East Qingchun Road, Hangzhou, Zhejiang, China.

institute: Department of General Surgery,Sir Run Run Shaw Hospital,School of Medicine,Zhejiang University

summary: Pancreatic cancer is one of the most aggressive tumors and has poor survival rates. Fisetin, a natural flavonoid, was recently reported to have antitumor effects in various cancer models. Autophagy is a conserved catabolic process that maintains cellular homoeostasis in response to stress, and together with apoptosis, determines cell fate. Herein, we examined the effect of fisetin on pancreatic cancer. We reveal that fisetin inhibits Panc-1 cell proliferation in vivo and in vitro. We found that AMPK-dependent autophagy was enhanced after fisetin treatment.However RNA-seq analysis revealed that the unfolded protein response, which is activated by ER stress, was enriched. We also found that there may be crosstalk between the AMPK- and p8-dependent pathways.

overall_design: Total mRNA profiles of human pancreatic cancer Panc-1 cells with or without treatment of Fisetin, were generated by deep sequencing, in triplicate.

first: S

last: Jia

first: X

last: Zhou

first: Y

last: Chen

first: G

last: Ding

first: L

last: Cao


title: Gene Expression Profiling of Cutaneous CD30+ Lymphoproliferative Disorders by RNA-seq

status: Public on Jan 25 2019

city: Beijing

first: Yang

last: Wang

address: Xishiku Street

institute: Peking University First Hospital

summary: Cutaneous CD30+ lymphoproliferative disorder (CD30+LPDs), including lymphomatoid papulosis (LyP) and primary cutaneous anaplastic large-cell lymphoma (PCALCL), comprises the second most common group of cutaneous T cell lymphoma. Previously, we reported that special AT-rich sequence-binding protein1 (SATB1), a thymocyte specific chromatin organizer, was over-expressed and promoted malignant T-cell proliferation in a portion of CD30+LPDs, whereas other CD30+LPDs didn't express SATB1 at all. To elucidate the underlying molecular events in CD30+LPDs with differential SATB1 expression, we subjected 4 SATB1+ and 3 SATB1- CD30+LPDs skin biopsies to second-generation RNA-sequencing (RNA-seq). These data provide a significant resource for studies of CD30+LPDs.

overall_design: 200ng total RNA samples were extracted and purified from 7 CD30+LPDs skin lesions (4 SATB1+, 3 SATB1-) to establish RNA library. Then the library was qualified through Agilent 2100 bioanalyzer instrument (Agilent Technologies, Santa Clara, CA) and Quantitative real-time polymerase chain reaction. The qualified library was sequenced on an Illumina HiSeqTM 2000 platform using paired-end reads. 10G raw data for each sample were obtained. The reads were aligned to the hg19 genome with SOAPaligner/SOAP2. Gene expression levels were calculated by reads per kilobase transcriptome per million mapped reads（RPKM）method.

first: Jingru

last: Sun


title: Nuclear Myosin I regulates genome stability by controlling p21 gene activation through a chromatin-based mechanism

status: Public on Jun 29 2019

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: Nuclear myosin 1 (NM1) has been implicated in key nuclear functions. Here, we show NM1 has a global role in chromatin regulation and this likely impacts global transcription. High-content phenotypic profiling and transcriptional profiling by RNA-Seq on NM1 KO mouse embryonic fibroblasts show extensive chromatin alteration and differential gene expression compared to a WT condition. In particular, NM1 deletion leads to significant upregulation of genes involved in DNA damage response and cell cycle, which is further supported by increased DNA damage revealed by increased γ-H2AX foci number and proliferation rate. We found that upon DNA damage, NM1 directly regulates expression of Cdkn1A (p21) and binds to p53. NM1 recruits histone acetyl-transferase PCAF and histone methyl-transferase Set1 to p21 promoter for histone H3 acetylation and methylation, facilitating Cdkn1A gene transcription.  We propose that NM1 regulates the transcriptional response upon DNA damage and imply an involvement for NM1 in genome stability.

overall_design: RNA seq of primary mouse embryonic fibroblast derived from E14 NM1 WT and KO embryos. 3 replicates for each group. Each replicate represents fibroblasts derived from three embryos.

first: Tomas

last: Venit

first: Nizar

last: Drou


title: Potential signaling pathways and gene signatures associated with brain metastases in NSCLC patients

status: Public on Feb 19 2019

city: Wuhan

first: Chunhua

last: Wei

address: 1277 JieFang Avenue

institute: Huazhong University of Science and Technology

summary: RNA-Seq analyses of various cancers have identified thousands of target genes that help guide clinical treatment. By using RNA-Seq analysis, we examined primary lung tumors from NSCLC patients with and without BM to identify differentially-expressed genes and potential signaling pathways in two groups. A total of 6 patients with histopathologically confirmed NSCLC (against AJCC criteria) were enrolled in the RNA-Seq study, 3 patients with BM and other 3 without BM. All the cancer tissues used in this study were taken from surgical specimens and biopsies, and preserved immediately in liquid nitrogen after surgery. Totally, 566 differentially-expressed genes between BM+ and BM- samples were identified by DESeq2 with log2Fold Change being more than 2 and P value of statistical test less than 0.05, 326 genes were significantly down-regulated and 240 genes were up-regulated in BM+ group.

overall_design: RNA isolation and RNA sequencing were performed in 6 NSCLC patients, 3 patients with BM and other 3 without BM. All libraries were sequenced on the Illumina Hiseq 2500 Sequencer.

first: Xiaomin

last: Dong

first: Xiaorong


title: CYTOGENETIC AND TRANSCRIPTOME PROFILING ANALYSIS OF MATCHED IN SITU/INVASIVE CUTANEOUS SQUAMOUS CELL CARCINOMAS FROM IMMUNOCOMPETENT PATIENTS [HuGene-2_0-st]

status: Public on Jan 03 2019

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

summary: Although most cutaneous squamous cell carcinomas (cSCC) develop from actinic keratoses (AK), the key events for this evolution remain unclear. We have combined the results of different genomic and expression array platforms on matched samples of sun-exposed skin, AK and cSCC from ten immunocompetent patients, with the objective of better understanding the mechanisms involved in this progression. Gene expression analysis and copy number alterations were assessed using GeneChip Human Gene 2.0 ST Array® (Affymetrix ) and CytoScan HD Cytogenetics Solution® (Affymetrix) platforms, respectively. Integration of genome and transcriptome results was evaluated using the DR-Integrator tool. Additional studies (qPCR, immunohistochemistry and Western blot) were performed for selected genes. Twenty-two genes showed a progressive expression spectrum from clinically normal sun-exposed skin samples to cSCC. FOSL1 and BNC1 encode transcription factors whose expression was increased in cSCC in the expression array and the qPCR. By immunohistochemistry, FOSL1 showed an intense staining at the invasive front of cSCC samples and BNC1 expression varied from a nuclear location (sun-exposed skin) to a cytoplasmic location (cSCC). Western blot analyses confirmed the enhancement of FOSL1 and BNC1 expression. Additionally, the smallest overlapping regions of genomic imbalance (SORIs) involving at least 3 of the samples of each group (sun-exposed skin, AK or cSCC) were selected. One of the SORIs was a deletion in the p24.1 band of chromosome 3, shared by 7 of the cSCC. A strong correlation in the integration analysis was found for NEK10, a gene contained in the previously mentioned SORI. Loss of NEK10 expression in cSCC was confirmed by immunohistochemistry and western blot analyses. In conclusion, our findings suggest that FOSL1 may play a role in promoting the cSCC invasion ability. We have also identified two additional genes, NEK10 and BNC1, which could also act as tumor drivers.

overall_design: A total of 30 samples were analyzed: 10 SES, 10 AKs and 10 cSCCs

first: Irene

last: García-Díez

first: Agustí

last: Toll

first: Inmaculada

last: Hernández-Muñoz

first: Eugenia

last: Hernández-Ruíz

first: Lara

last: Nonell

first: Eulàlia

last: Puigdecanet

first: Marta

last: Bódalo-Torruella

first: Evelyn

last: Andrades

first: Ramón

last: Pujol


title: CYTOGENETIC AND TRANSCRIPTOME PROFILING ANALYSIS OF MATCHED IN SITU/INVASIVE CUTANEOUS SQUAMOUS CELL CARCINOMAS FROM IMMUNOCOMPETENT PATIENTS

type: Genome variation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Global gene expression changes in the lung and ileum of hyperoxia-exposed neonatal mice

status: Public on Jan 24 2019

city: Birmingham

first: Tamas

last: Jilling

state: AL

address: UAB Station

department: Department of Pediatrics

institute: The University of Alabama at Birmingham

summary: Ths study addressed the hypothesis that exposure to hyperoxia alters gene expression in both the lung and the ileum, but that the gene epxression cahnges are specific to each organ.  The data indicat ethat there are highly specific changes in each organ due to hyperoxia.

overall_design: Neonatal mice were exposed from postnatal day 3 (P3) to P14 to either normoxia (FiO2=21%) or hyperoxia (FiO2=85%). Global changes of gene expression in the lung and ileum were analyzed by Illumina microarray.

first: Namasivayam

last: Ambalavanan


title: CYTOGENETIC AND TRANSCRIPTOME PROFILING ANALYSIS OF MATCHED IN SITU/INVASIVE CUTANEOUS SQUAMOUS CELL CARCINOMAS FROM IMMUNOCOMPETENT PATIENTS [CytoScanHD_Array]

overall_design: A total of 40 samples were analyzed: 10 SES, 10 AKs, 10 cSCCs and 10 peripheral blood (PB) samples


title: ImmGen ULI RNA-seq data

status: Public on Feb 27 2019

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

summary: Primary RNAseq data from carefully sorted immunocyte populations, sequenced using ImmGen's SOP for 'ultra-low-input' population RNAseq (typically 500 to 1,000 cells) performed by Smartseq2.

overall_design:
This Superseries is an umbrella for all datasets generated by ImmGen labs using a joint low-input population RNAseq protocol. The actual datasets that use this joint protocol are listed below.

In practice, cell samples collected across ImmGen participating labs (or collaborating labs for OpenSource projects) are prepared to very high purity (2 rounds or more of cell sorting) using the ImmGen SOP (immgen.org; see below). After direct lysis, samples are frozen and shipped to the ImmGen Core team for common library construction and sequencing using ImmGen's standard RNA-seq (SmartSeq2) pipeline at the Broad Institute’s Technology Lab.

After the final sort of 500 to 1,000 cells directly into 5ul lysis buffer (TCL Buffer (Qiagen) with 1% 2- Mercaptoethanol), Smart-seq2 libraries were prepared as previously described (Picelli et al., 2013; Picelli et al., 2014) with slight modifications. Briefly, total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5'AAGCAGTGGTATCAACGCAGAGTACT30VN-3') and converted to cDNA via reverse transcription. First strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 18 cycles using barcoded primers such that each sample carries a specific combination of eight base Illumina P5 and P7 barcodes and pooled together prior to Smart sequencing. Smart-seq paired-end sequencing was performed on an Illumina NextSeq500 using 2 x 25bp reads with no further trimming.


title: Global gene expression profiles of basophils isolated from human blood after engagement of immunoglobulins on their surface.

status: Public on Dec 31 2018

summary: Basophils are blood leukocytes associated to Th2 responses and allergy reactions primarily through the IgE bound to their surface throught the Fc Epsilon hifh affinity receptor. Soluble IgD is an enigmatic antibody isotype whose function remains elusive. We have characterised the presence of this antibody isotype on the surface of basophils where we hypothesise that it plays a role in Th2 responses and allergy reactions.

overall_design: Basophils from peripheral blood from 3 donors were MACS sorted (Basophil isolation Kit II, Milteny) and to increase purity we performed negative FACSorting using lineage-specific antibodies (CD3, CD14, CD19, CD56) (Final purity >98%). These were either untreated or treated with anti-IgE, anti-IgD or both, for 20 minutes at 37º before proceeding to RNA extraction.

first: Cerutti

last: Andrea

first: Yeste

last: Ada


title: Immunoglobulin sequencing of Lyme disease individuals

status: Public on Dec 21 2018

city: Stanford

first: Lisa

middle: K

last: Blum

address: 269 Campus Drive

institute: Stanford University


title: Comparison of the response to the TNF  treatment in C57BL6 and sst1 knockout TB resistant mouse macrophages

status: Public on Jan 01 2019

first: Alexander

last: Gimelbrant

state: Massachusetts

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute and Harvard Medical School

summary: Macrophages derived from the wt and 1h mice were treated with the increasing concentrations of the TNF followed by the RNA-Seq analysis.

overall_design: Examination of the response of the macrophages derived from two different mouse strains  to the TNF treatment

first: Igor

last: Kramnik

first: Sujoy

last: Chatterjee

first: Bidisha

last: Bhattacharya

first: Anwesha

last: Nag

first: Kyomi

last: Igarashi

first: Marina

last: Kasaikina

first: Denis

last: Lafontaine


title: Single cell paired heavy- and light-chain immunoglobulin sequencing of sorted Lyme disease plasmablasts

summary: Lyme disease (Borrelia burgdorferi infection) is increasingly recognized as a significant source of morbidity world-wide. Here, we investigated B cell responses to Lyme disease through barcode-enabled single cell sequencing of activated B cells (plasmablasts) sorted from PBMCs. Bulk immunglobulin heavy-chain sequencing from this project has also been separately deposited. Additional information regarding patient characteristics and overlap with other data from the SLICE study is available upon request.

overall_design:
Single cell sequencing of plasmablast antibody genes was performed as previously described (Blum 2018, DOI: 10.1002/eji.201747460)
Lyme disease timepoints: Visit 1, Untreated acute infection; Visit 3, one month after completion of treatment; Visit 5, six months after treatment; Visit 7, two years after treatment.
Healthy control timepoints: Visit H1, initial visit; Visit H2, six months after initial; Visit H3, one year after initial visit.
Plasmablasts were single-cell sorted into the wells of a 96-well plate (1-16 plates per timepoint, per subject) and cDNA waere tagged with unique well-ID barcodes by template switching during reverse transcription.
Wells were pooled from within each plate, pooled samples were amplified with immunoglobulin gene-specific primers, and plate-specific index sequences added during library preparation
Libraries of up to 48 plates per run were sequenced with MiSeq 2x330 paired-end sequencing

first: William

middle: H

last: Robinson

first: Alison

last: Rebman


title: Generation of esophageal organoids from human pluripotent stem cells and their use to study human development

status: Public on Jul 01 2018

city: Cincinnati

first: James

last: Wells

state: OH

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hospital Medical Center

summary: Tracheoesophageal disorders and diseases are prevalent in humans such that an organoid model of human esophagus could be greatly beneficial. We therefore established a three-dimensional esophageal organoid culture system through the directed differentiation of human pluripotent stem cells (hPSCs). We identified that sequential manipulation of several signaling pathways resulted in patterning of definitive endoderm to dorsal anterior foregut spheroids (dAFGs). Outgrowth of dAFGs for 1-2 months resulted in human esophageal organoids (HEOs) with a stratified squamous epithelium comparable to a late gestation mouse embryonic esophagus. These 1 and 2 month old HEOs were harvested for RNA to transcriptionally profile and compare them to profiles of esophageal tissue biopsies and keratinocytes. We then used HEOs and mouse embryos to identify how SOX2 mediates separation of the esophageal and respiratory lineages and found that loss of endodermal Sox2 results in complete esophageal agenesis. Using a SOX2 CRISPR interference iPS line, we generated dorsal and ventral anterior foregut progenitors (by manipulating BMP signaling) with or without SOX2-knockdown. At the transcriptional level, SOX2 acts to promote esophageal specification in both mice and humans in part by inhibiting Wnt signaling in the dorsal AFG and promoting survival of esophageal epithelium. In addition to this use of hPSC-derived esophageal organoids to study development, HEOs can be used for future studies of esophageal pathologies, such as Barrett’s metaplasia and carcinoma.

overall_design: Human pluripotent stem cells (H1 line) were differentiated into human esophageal organoids (HEOs) and harvested at 1 and 2 months. Induced pluripotent stem cells (iPS CRISPRi-SOX2 line) were differentiated to dorsal or ventral anterior foregut cultures by manipulating BMP signaling (Noggin or BMP4) and treated with or without doxycycline (1ug/mL) to induce expression of CRISPR interference construct. For all experiments, total RNA was extracted, and polyA-selected libraries was generated and sequenced.

first: Stephen

middle: L

last: Trisno

first: Katherine

last: Philo

first: Praneet

last: Chatuvedi

first: Mohammad

last: Mandegar


title: THE POLYCOMB PROTEINS RING1B AND EZH2 REPRESS THE TUMORAL PROINFLAMMATORY FUNCTION IN METASTASIZING PRIMARY CUTANEOUS SQUAMOUS CELL CARCINOMA

status: Public on Jun 04 2018

first: Júlia

last: Perera-Bel

summary: Cutaneous squamous cell carcinoma (cSCC) is the second most common malignancy in humans and approximately 5% metastasize, usually to regional lymph nodes. Epigenetic regulation of gene expression may allow tumoral cells to acquire new functions in order to escape from the primary tumor. The aim of this study was to investigate the expression and function of proteins of the Polycomb family of epigenetic regulators in the metastatic process of cSCC. A higher expression of RING1B and EZH2 was detected by immunohistochemistry in  a  series  of  primary  cSCC  tumors  that  metastasized  (MSCC)  when  compared  to  non metastasizing  cSCC  (non MSCC).  Stable  downregulation  of  RING1B  and  EZH2  in  cSCC cells results in enhanced expression of inflammatory cytokines and activation of the NFκB signaling  pathway.  Accordingly,  non MSCC  display  higher  levels  of  membranous  pS176 IKK and their stroma is enriched in neutrophils and eosinophils when compared to MSCC. In vitro,  hematopoietic  cells  exhibit  a  substantial  migratory  response  to  supernatants  from Polycomb depleted  cSCC  cells. Altogether  these  data indicate  that  RING1B  and  EZH2 repress  the  innate  inflammatory  cSCC  function  and  impair  tumor  immunosurveillance  and suggest that patients with high risk cSCC could benefit from clinical therapies addressed to harness the immune response.

overall_design: 8 samples were analyzed: shBMI1 (n=2); shGFP (n=2); shRING1b (n=2); shEZH2 (n=2);

first: María

last: Inmaculada

first: Hernández

last: Muñoz

first: Agusti

last: Toll


title: Systematic immune reprogramming via PD-1 inhibition enhances early-stage lung cancer survival.

status: Public on Jul 26 2018

city: New York

first: Olivier

last: Elemento

address: 1305 York Ave

department: Biochemistry

institute: Weill Cornell Medicine

summary: Success of immune checkpoint inhibitors in advanced non-small cell lung cancer (NSCLC) has invigorated their use in neo-adjuvant setting for early-stage disease. However, the cellular and molecular mechanisms of the early immune responses to therapy remain poorly understood. Through an integrated analysis of early-stage NSCLC patients and a Kras-mutant mouse model, we show a prevalent programmed cell death 1/ programmed cell death 1 ligand 1 (PD-1/PD-L1) axis exemplified by increased intratumoral PD-1+ T cells and PD-L1 expression. Notably, tumor progression was associated with spatiotemporal modulation of the immune microenvironment. Importantly, PD-1 inhibition controlled tumor growth, improved overall survival, and reprogrammed tumor-associated lymphoid and myeloid cells. Depletion of T lymphocyte subsets demonstrated synergistic effects of those populations on PD-1 inhibition of tumor growth. Transcriptome analyses revealed T cell subset-specific alterations corresponding to degree of response to the treatment. These results provide insights into temporal evolution of the phenotypic effects of PD-1/PD-L1 activation and inhibition, and motivate targeting this axis early in lung cancer progression.

overall_design: CD4 and CD8 lung tumor infiltrating lymphocytes were sorted into RLT lysis buffer from IgG antibody or anti-PD1 antibody treated C57Bl/6 mice at day 14, 17 or 24 for mRNA-Sequencing.

first: Vivek

last: Mittal

first: Geoffrey

last: Markowitz


title: The scaffolding role of RNA in ribonucleoprotein complexes: TRA2A recruitment in FXTAS disease

status: Public on Jun 19 2018

summary: To address the functional implications at highthroughput level of TRA2A recruitment in FXTAS nuclear inclusions we performed Clariom D splicing arrays with the COS-7 cell models. We compared the profiles of the cells upon CGG overexpression, TRA2A overexpression and knockdown, with the respective controls.

overall_design: 18 samples were analyzed: controls (n=3); cond1 (n=3);  cond2  (n=3);  cond3 (n=3);  cond4 (n=3); cond5 (n=3)

first: Teresa

last: Botta-Orfila

first: Mariona

last: Gelabert-Baldrich

first: Gian

last: Tartaglia


title: EphA2 receptor is a key player in the metastatic onset of Ewing sarcoma

status: Public on Apr 11 2018

summary: Ewing sarcoma (ES) is the second most common bone malignancy affecting children and young adults with poor prognosis due to high metastasis incidence. Our group previously described that EphA2, a tyrosine kinase receptor, promotes angiogenesis in ES cells via ligand-dependent signaling. EphA2 ligand-independent activity, controlled upon phosphorylation at S897 (p-EphA2S897), has been linked to metastasis in several malignancies. Here, we stablish a correlation between ES cells aggressiveness and p-EphA2S897. Moreover, stable overexpression of EphA2 in low EphA2 expression ES cells enhanced proliferation and migration, but not a nonphosphorylable mutant (S987A). Consistently, silencing of EphA2 reduced tumorigenicity, migration and invasion in vitro, and lung metastasis incidence in experimental and spontaneous metastasis assays in vivo. A gene expression microarray revealed the implication of EphA2 in cell signaling, cellular movement and survival. Altogether, our results suggest that p-EphA2S897 correlates with aggressiveness in ES, so blocking its function may be a promising treatment.

overall_design: 9 samples were analyzed: A673 parental or transfected with control shRNA (n=2); TC252 parental or transfected with control shRNA (n=2); A673 transfected with EphA2 shRNA (n=2), TC252 transfected with EphA2 shRNA (n=3),

first: Silvia

last: Garcia-Monclús

first: Oscar

last: Tirado


title: Gene expression in tissues of SHR and SHRSP compared with WKYs treated with 2K1C or 1K1C, or without operation for 3 weeks at 6 weeks of age

status: Public on Mar 21 2019

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.


title: MiCEE: a ncRNA-protein complex mediates epigenetic silencing and nucleolus organization

status: Public on Apr 06 2018

city: Nancy Cedex

first: Guillermo

last: Barreto

address: 9, Avenue de la Forêt de Haye ‐ BP 20199

department: Campus Biologie-Santé. Faculté de Médecine

institute: CNRS Director of Research

summary: The majority of the eukaryotic genome is transcribed into non-coding RNAs (ncRNAs), which are important regulators of different biological processes in the cell nucleus as part of the machinery controlling chromatin structure. However, the full extent of ncRNAs function has remained elusive. Here we deciphered the function of the microRNA Mirlet7d as a key regulator of the expression of bi-directionally transcribed genes. We found that nuclear Mirlet7d binds  ncRNAs expressed from these genes. The  Mirlet7d-ncRNA duplexes are further bound by C1D,  which in turn targets the RNA exosome complex and EZH2 to the bi-directionally active loci. The exosome degrades the ncRNAs, whereas EZH2 induces heterochromatin and transcriptional silencing. Moreover, this multicomponent RNA-protein complex, which we called MiCEE,  tethers the regulated genes to the perinucleolar region, thereby being required for proper nucleolus organization. Our study demonstrates that the MiCEE complex mediates epigenetic silencing of bi-directionally expressed genes and global genome organization.

overall_design:
RNA_Seq Data from MLE-12 cells:
i)  Investigate the effect of Mirlet7d gain-of-function on the RNA population in the nucleus of the cell.
ii) Pulldown experiment to identify the RNAs that interact with Mirlet7d in the nucleus of the cell.
RNA-seq after Mirlet7d-Pulldown, RNA-seq after Mirlet7d-GOF, Mirlet7d-ChIRP-seq and small_RNA_Seq from MLE-12 cells


title: Expression data from MMTV-PyMT Induced Tumors

status: Public on Feb 22 2018

city: East Lansing

first: Daniel

middle: Patrick

last: Hollern

state: MI

address: 2194 Biomedical Physical Sciences

institute: Michigan State University

summary:
Loss of E2F transcription factos alters metastatic capacity of MMTV-PyMT tumors.
We used microarrays to futher characterize the effects of E2F loss on mammary tumorigenesis in MMTV-PyMT mice.

overall_design: 80 MMTV-PyMT mammary tumors were used for RNA extraction and hybridization on Affymetrix microarrays.

middle: P

first: Eran

last: Andrechek


title: Analysis of RNA-seq libraries for conditional knock-out of transcription factors in adult mouse pancreas

city: Dallas

first: Galvin

last: Swift

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: U TX Southwestern Medical Center

summary: The purpose of this study is to determine the roles and hierarchy of the transcription factors Foxa2, Gata4, Nr5a2, and Ptf1a in the control of the physiology of the adult exocrine pancreas.  Knockouts of each gene were induced by tamoxifen treatment of mice bearing a Ptf1aCreER allele as well as floxed alleles of the gene(s) to be knocked out.  Four to eight RNA-seq libraries were analyzed for control animals, knockouts of each single gene, pairwise knockouts of Ptf1a & Foxa2, Ptf1a & Gata4, Ptf1a & Nr5a2, Foxa2 & Gata4, Gata4 & Nr5a2, and a four gene knockout of Ptf1a, Foxa2, Gata4, and Nr5a2 (eleven different genotypes in all).

overall_design:
Each RNA-seq library was synthesized from pancreas RNA

This series includes the re-analysis of three samples from GSE86261 (GSM2299174, GSM2299175 and GSM2299181).

first: Ana

last: Azevedo-Pouly

first: Raymond

last: MacDonald


title: RNA-seq reveals abundant circRNA, lncRNA and mRNA in blood exosomes of patients with hepatocellular carcinoma

city: Shanghai

first: Shengli

last: Li

address: 650 Xinsongjiang Road

institute: Shanghai Jiao Tong University School of Medicine

summary: Exosomes are small membrane vesicles of endocytic origin secreted by most cells, and contain a wealthy cargo of protein and RNA species that can modulate recipient cells’ behaviors and may be used as biomarkers for diagnosis of human diseases. They have been found in blood and are valuable sources for biomarkers due to selective cargo loading and resemblance to their parental cells. The goal of this study is to identify circRNA, lncRNA and mRNA profiles in human blood by high-throughput RNA sequencing (RNA-seq). 1-4 ml plasma or serum were used to extract exosomal RNAs by exoRNeasy Serum/Plasma Maxi kit (Qiagen). The exosomal RNAs were further treated with DNAse I and subjected to ribosome minus low-input RNAseq library preparation. The libraries were sequenced by Illumina Hiseq platform.

overall_design: Human blood exosomal RNAs were generated by deep sequencing using Illumina Hiseq.

first: Lu

last: Wang


title: RNA-seq reveals abundant circRNA, lncRNA and mRNA in blood exosomes of patients with pancreatic carcinoma

address: 270 Dong An Road

institute: Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences

first: Shulin

last: Yu

first: Peng


title: Spatio-temporal structure of cell fate decisions in murine neural crest

status: Public on Apr 02 2019

first: Ruslan

last: Soldatov

state: New York

address: 323 E 61st Street

department: Computational Oncology

institute: Memorial Sloan Kettering Cancer Center

summary: Neural crest cells are embryonic progenitors that generate numerous cell types in vertebrates. With single cell analysis, we show that mouse trunk neural crest cells become biased toward neuronal lineages when they delaminate from the neural tube, whereas cranial neural crest cells acquire ectomesenchyme potential dependent on activation of the transcription factor Twist1. The choices that neural crest cells make to become sensory, glial, autonomic, or mesenchymal cells can be formalized as a series of sequential binary decisions. Each branch of the decision tree involves initial co-activation of bipotential properties followed by gradual shifts towards commitment. Competing fate programs are co-activated before cells acquire fate-specific phenotypic traits. Determination of a specific fate is achieved by increased synchronization of relevant programs and concurrent repression of competing fate programs.

overall_design: Analysis of neural crest developmental landscape using single-cell expression profiling across developmental stages and rostro-caudal  axis

first: Marketa

last: Kaucka

first: Maria

last: Kastriti

first: Peter

middle: V

last: Kharchenko

first: Igor

last: Adameyko


title: RNA-seq reveals abundant circRNA, lncRNA and mRNA in blood exosomes of patients with colorectal carcinoma

first: Jiang

last: Zhao

first: Ye

last: Xu


title: FABP4 overexpressed in intratumoral hepatic stellate cells within hepatocellular carcinoma with metabolic risk factors (part 3)

status: Public on Jan 28 2018

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 2-1-1 Hongo

department: Intractable Disease Research Center

institute: Juntendo University

summary: BACKGROUND & AIMS: Metabolic syndrome is a newly identified risk factor for hepatocellular carcinoma (HCC), however the molecular mechanisms still remain unclear. To elucidate this issue, cross-species analysis was performed to compare gene expression patterns of HCC from human patients and melanocortin 4 receptor-knockout (MC4R-KO) mice, developing HCC with obesity, insulin resistance and dyslipidemia.  METHODS: Unsupervised hierarchical clustering and principle component analysis of 746 differentially expressed orthologous genes classified HCC of 152 human patients and MC4R-KO mice into two distinct subgroups, one of which included all the mouse HCC was etiologically associated with metabolic risk factors, such as obesity and diabetes. A specific biomarker was identified by the integrative analysis, and validated with in vitro studies and other cohort patients.  RESULTS: As commonly overexpressed in human and mouse metabolic disease-associated HCC, FABP4 was remarkably enriched in intratumoral activated hepatic stellate cells (HSCs). Then, we established subclones constitutively expressing FABP4 from a human HSC cell line, in which the expression levels of inflammatory chemokines including IL1A and IL6 was upregulated through NF-κB nuclear translocation. An immunohistochemical validation study of other 106 human HCC samples indicated that FABP4-positive HSCs were distributed in tumors of 38 cases, and that the FABP4-high group was composed of patients with non-viral and non-alcoholic HCC (P=0.027) and with multiple metabolic risk factors (P<0.001) compared with the FABP4-low.  CONCLUSIONS: FABP4 overexpression in HSCs could contribute to hepatocellular carcinogenesis in patients with metabolic risk factors via modulation of inflammatory pathway, and is a promising novel biomarker as well as a potential therapeutic target for this subtype of HCC.

overall_design: A total of 152 patients who underwent curative hepatic resection for HCC between 2006 and 2011 at Tokyo Medical and Dental University Hospital participated in integrated gene expression microarray analysis. Fourteen adjacent liver tissues obtained from patients with metastasis of colorectal cancer who had not received chemotherapy were used as control.

first: Norimichi

last: Chiyonobu

first: Shu

last: Shimada

first: Yoshimitsu

last: Akiyama

first: Michiko

last: Itoh

first: Keiichi

last: Akahoshi

first: Satoshi

last: Matsumura

first: Kosuke

last: Ogawa

first: Hiroaki

last: Ono

first: Yusuke

last: Mitsunori

first: Daisuke

last: Ban

first: Atsushi

last: Kudo

first: Shigeki

last: Arii

first: Takayoshi

last: Suganami

first: Shoji

last: Yamaoka

first: Yoshihiro

first: Minoru

last: Tanabe

first: Shinji

last: Tanaka


title: FABP4 overexpressed in intratumoral hepatic stellate cells within hepatocellular carcinoma with metabolic risk factors (part 2)

first: Kaoru

last: Mogushi

first: Norimichi


title: FABP4 overexpressed in intratumoral hepatic stellate cells within hepatocellular carcinoma with metabolic risk factors (part 1)

last: Chiyonobu

first: Shu

first: Yoshimitsu


title: ImmGen ULI: Systemwide RNA-seq profiles (#1)

status: Public on Jan 13 2018

first: Liang

last: Yang

summary: Primary RNAseq data for 127 highly purified immunocyte populations representing all lineages and several differentiation cascades, profiled using the ImmGen ULI pipeline.

overall_design:
These RNAseq profiles were generated by ImmGen labs in a combined study associating RNAseq and ATACseq performed on cell populations sorted in parallel (companion ATACseq datasets are found in GSE100738). The 127 cell populations include all adaptive and innate lymphocytes (B, abT, gdT, Innate-Like Lymphocytes), myeloid cells (dendritic cells, macrophages, monocytes), mast cells and neutrophils. Most were prepared from baseline unchallenged mice, some after cell activation (LPS, anti-CD3, viral infection). For B and T lymphocytes, many successive steps of their known differentiation cascades in the thymus and bone marrow are included.
----------------------------------------
Immunological Genome Project Consortium


title: FABP4 overexpressed in intratumoral hepatic stellate cells within hepatocellular carcinoma with metabolic risk factors

status: Public on Jan 27 2018

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

overall_design: Refer to individual Series


title: Definition of human cardiac progenitor cell plasma membrane signature: comparative genomic and proteomics analysis with human mesenchymal stem cells

status: Public on Oct 31 2017

city: Madrid

first: Carlos

last: Torroja

state: Madrid

address: Melchor Fernandez Almagro, 3

department: Bioinformatics Unit

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

summary: Adult cardiac progenitor/stem cells (CPC/CSC) are multipotent resident populations involved in cardiac homeostasis and heart repair. Assisted by complementary RNAseq analysis, we defined the proteome fraction associable to specific CPC functions by comparison with human mesenchymal stem cells (MSC), the reference population for cell therapy. Label-free proteomics analysis identified 526 proteins expressed differentially in CPC. Quantitative iTRAQ analysis confirmed differential expression of a substantial proportion of these proteins expressed specifically in CPC relative to MSC. Systems biology analysis defined a clear overrepresentation of several categories related to enhanced angiogenic potential. The CPC plasma membrane compartment is comprised by 1595 proteins including a minimal signature of 167 proteins expressed preferentially in CPC. Of these core CPC functions, we selected a panel of 15 predicted cell surface markers and validated high differential expression of CDH5, CD200 and F11R in CPC.

overall_design: RNA was isolated from CPC (CPC1 (H1), CPC2 (H3), CPC3 (H4)), MSC (MSC1 (19), MSC2 (33)), MSC3 (45) and HDF (FB1, FB2, FB3) as described (Moscoso et al., 2013).  For RNAseq library production, total RNA (1 μg) was used with the TruSeq RNA Sample Preparation v2 Kit (Illumina) to construct index-tagged cDNA libraries. Libraries were sequenced (single-end mode, 75 bp length) on the Genome Analyzer IIx following the standard RNA sequencing protocol, with the TruSeq SBS Kit v5.  Fastq files containing reads for each library were extracted and demultiplexed using the Casava v1.8.2 pipeline

first: José

last: Torán

first: Juan

middle: A

last: López

first: Patricia

last: Gomes-Alves

first: Susana

last: Aguilar

first: Mario

last: Trevisán-Herranz

first: Isabel

last: Moscoso

first: Maria

last: Sebastiã

first: Margarida

last: Serra

first: Catarina

last: Brito

last: Sepúlveda

last: Abad

first: Fernando

last: Martínez

first: Luis

last: R-Borlado

first: Jesús

last: Vázquez

first: Paula

middle: M

last: Alves

first: Antonio

last: Bernad


title: Cathelicidin-deficient mice exhibit increased survival and upregulation of key inflammatory response genes following cecal ligation and puncture

status: Public on Jun 20 2017

city: Sao Paulo

last: Severino

state: Sao Paulo

address: Rua Comendador Elias Jafet, 755

department: Albert Einstein Research and Education Institute

country: Brazil

institute: Hospital Israelita Albert Einstein

summary: Antimicrobial peptides possess a myriad of molecular properties including bacterial killing and the regulation of many aspects of innate immunity. Cathelicidins are a group of antimicrobial peptides widely investigated by the scientific community. Many studies have focused on the bactericidal and pro-inflammatory roles of cathelicidins. Because the role of endogenous cathelicidin expression remains obscure in deep-seated systemic infections, we induced sepsis in cathelicidin knockout and wild-type (WT) mice by cecal ligation and puncture, performing transcriptome screening by DNA microarray in conjunction with other immunologic assays. Cathelicidin-deficient mice showed increased survival compared to WT mice in this established experimental model of polymicrobial sepsis, in association with upregulation of certain key inflammatory response genes. Therefore, cathelicidins can exert both pro- and anti-inflammatory activities depending on the disease and cellular context.

overall_design: We induced sepsis in cathelicidin-deficient mice, using the cecal ligation and puncture model (CLP), and compared their mortality and gene expression patterns to wild-type controls.

first: Suely

last: Ariga

first: Hermes

last: Barbeiro

first: Thais

last: de Lima

first: Elisangela

last: Silva

first: Denise

middle: F

first: Marcel

last: Machado

first: Victor

last: Nizet

first: Fabiano

last: da Silva


title: Transcriptome of human B cell subsets isolated from terminal ileum and spleen

status: Public on Jul 27 2017

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

institute: Hospital del Mar Research Institute

summary: Non-switched memory (ME-M) B cells are an enigmatic population of IgM+ memory lymphocytes that are thought to emerge from germinal centers during systemic antibody responses against T cell-dependent antigens. To gain new insights into the properties of ME-M B cells generated during intestinal antibody responses, we performed global gene transcriptome expression analysis on naïve, ME-M and canonical memory class-switched (ME-SW) B cells purified from human gut samples. Marginal zone (MZ) and ME-SW B cells isolated from human spleen samples were used for comparison.

overall_design: Naive (N) B cells (CD45+CD19+CD38-CD10-IgD++IgM+CD27-), MZ B cells (CD45+CD19+CD38-CD10-IgD+IgM++CD27+), ME-M B cells (CD45+CD19+CD38-CD10-IgD-IgM+CD27+) as well as ME-SW B cells (CD45+CD19+CD38-CD10-IgD-IgM-) were FACSorted from histologically normal tissue samples obtained from human terminal ileum (4 adult donors undergoing right hemicolectomy) and/or human spleen (4 adults donors).

first: Andrea

last: Cerutti

first: Giuliana

last: Magri

first: Laura

last: Comerma


title: Adult parotid gland RNA-seq libraries, and embryonic submandibular gland RNA-seq libraries

status: Public on Aug 18 2017

first: Galvin

last: Swift

summary: Adult parotid gland RNA-seq libraries and embryonic submandibular gland RNA-seq libraries were created to examine the mRNA species present in these secretory glands, as part of a project to understand acinar glands in general.

overall_design: For adult animals, each RNA-seq library was synthesized from parotid RNA of a single animal. For embryonic samples, each library was synthesized from submandibular gland RNA isolated from pools of dissected glands.

first: Raymond

last: MacDonald

first: Travis

last: Wilson


title: Differential gene expression analysis of peripheral blood leukocytes reveals overexpression of tumor progression-related genes in patients with intra-abdominal infection after surgery for colon cancer: a prospective matched cohort study

status: Public on Jun 12 2017

summary: The aim was to investigate the effect of postoperative intra-abdominal infection on the gene expression patterns of peripheral blood leukocytes (PBL) after surgery for colorectal cancer

overall_design: Prospective matched cohort study. Patients who had an anastomotic leak or intra-abdominal abscess were included in the infection group (n=23). For each case patient, another patient with an uncomplicated postoperative course was selected for the control group (n=23). Some other unmatched samples are included in this data set

first: Miguel

last: Pera

first: Sandra

last: Alonso


title: RNA-seq reveals abundant circRNA, lncRNA and mRNA in blood exosomes of normal persons

status: Public on Jun 19 2017

first: Shengli

last: Li

first: Shenglin

last: Huang


title: HSV1 transcriptosome analysis by PAcBio long read sequencing

status: Public on Jul 12 2017

city: Szeged

first: Attila

last: Szűcs

address: Somogyi utca 4

department: Faculty of Medical Research

country: Hungary

institute: University of Szeged

summary: In this study, we used the amplified isoform sequencing technique from Pacific Biosciences to characterize the poly(A) fraction of the lytic transcriptome of the herpes simplex virus type 1 (HSV-1). Our analysis detected 34 formerly unidentified protein-coding genes, 10 non-coding RNAs, as well as 17 polycistronic and complex transcripts. This work also led us to identify many transcript isoforms, including 13 splice and 68 length variants, as well as several transcriptional overlaps. Additionally, we determined previously unascertained transcriptional start and polyadenylation sites. We analyzed the transcriptional activity from the complementary DNA strand in five convergent HSV gene pairs with quantitative RT-PCR and detected antisense RNAs in each gene. This part of the study revealed an inverse correlation between the expressions of convergent partners. Our work adds new insights for understanding the complexity of the pervasive transcriptional overlaps by suggesting that there is a crosstalk between adjacent and distal genes through interaction between their transcription apparatuses. We also identified transcripts overlapping the HSV replication origins, which may indicate an interplay between the transcription and replication machineries. The relative abundance of HSV-1 transcripts has also been established by using a novel method based on the calculation of sequencing reads for the analysis.

overall_design: 6 different mRNA isolation and/or size selection protocol were used to discover novel new mRNA isoforms in Herpes simplex virus 1 infected Vero cells.

first: Dora

last: Tombacz

first: Norbert

last: Moldovan

first: Zsolt

last: Csabai

last: Balazs

last: Szucs

first: Mike

last: Snyder

last: Boldogkoi


title: Human lymph node derived fibroblastic and double negative reticular cells alter their chemokines and cytokine expression profile following inflammatory stimuli

first: Patricia

last: Severino

summary: Lymph node is a secondary lymphoid organ that has structural organization related to their immune function, which is highly ordered and compartmentalized. Lymph nodes shelter immune cells and also fibroblastic-like cells such as fibroblastic reticular cells (FRCs). FRCs have mesodermal origin and are classically characterized by the expression of podoplanin (PDPN/gp38) and lack of CD31 expression. FRCs are implicated in several immune processes but the pathways subjacent their function are still a matter of research. Another cell population found in LNs, the double negative cells (DNCs), are even less known. They do not express PDPN or CD31 markers and a specific marker is absent, their localization within the LN is undefined and their phenotype or function, remain to be clarified. Although these cells have been studied in murine models, studies on human FRCs and DNCs are limited and therefore our study should contribute to the understanding of biology and function of these cells and should promote knowledge of efficiency and disorders in the lymph node immune response. This study evaluates gene expression and secretion of cytokines and chemokines in human-derived FRCs and DNCs during homeostasis and following inflammatory stimuli. Our results demonstrate that cytokines and chemokines secreted by human FRCs and DNCs partially differ from those identified in murine models. In addition, our study demonstrates that DNCs expressed a more varied of cytokines when compared with FRCs, while FRCs expressed a wider chemokines pattern. Such differences maybe related with specific functional differences between those cell populations within LNs.

overall_design: Peripheral (PLN) and mesenteric human LN (MLN) were obtained from 04 individuals with different ages and clinical status (larynx cancer-LN03, diverticulitis-LN12, breast cancer-LN15 patients and a liver donor-LN16) submitted to surgical procedures.The FRCs and DNCs were cultured with or without inflammatory stimuli provided by TNFα (25ng/mL) in combination with IL-1β (5ng/mL) treatments (17, 18). The culture supernatant was removed 24 hours after treatment and frozen for ELISA assays.  The cells that remained attached to the culture plate were harvested for RNA extraction. In total 4 LNs were used for gene expression analysis, 2 LNs isolated from cancer patients (LN04 and LN15), 1 from a diverticulitis patient (LN12) and 1 isolated from a healthy liver donor (LN16). We compared treated and control FRCs and DNCs: cells were treated or not with INF-γ (50ng/mL) or TNFα (25ng/mL) in combination with IL-1β (5ng/mL).

first: Diana

last: Torres Palomino

first: Heliene

last: Alvarenga

first: Camila

last: Bononi Almeida

first: Denise

last: Cunha Pasqualim

first: Adriano

last: Cury

first: Paolo

last: Salvalaggio

first: Antonio

last: Macedo

first: Silvio

last: Bromberg

first: Luiz

last: Rizzo

first: Luciana

last: Marti


title: Genomic and Epigenomic Profiling of High-Risk Intestinal Metaplasia Reveals Molecular Determinants of Gastric Cancer Progression

status: Public on Jan 09 2018

city: Singapore

first: Kie Kyon

last: Huang

state: Select State/Province

address: 8 College Road

country: Singapore

institute: Duke-NUS Graduate Medical School

summary: Metaplasia of the gastric epithelia (intestinal metaplasia, IM) is a pre-malignant lesion associated with increased gastric cancer (GC) risk.

overall_design: Bisulphite converted DNA from the 191 samples were hybridised to the Illumina Infinium Human Methylation 450K Beadchip

first: Kie

first: Tan

last: Patrick


title: Stem cell regulatory elements remain bookmarked by selected transcription factors and epigenetic marks during mitosis

status: Public on May 16 2017

first: Effie

last: Apostolou

state: NY

address: 1161 York Avenue, Apt 8A

summary:
Purpose: We investigated the existence, nature and significance of mitotic bookmarking of Klf4, Oct4, Sox2 (KOS) and H3K27ac in mouse ESCs.
Methods: DNA-binding/epigenetic profiles of KOS and H3K27ac on asynchronous and mitotic chromatin were generated by deep sequencing following chromatin immunoprecipitation, in replicates.
Results: KOS and H3K27ac are largely maintained on mitotic chromatin. KOS bookmark critical stem cell regulatory elements during mitosis. H3K27 acetylation during mitosis is highly retained on promoters of cell cycle and homeostasis related genes and enhancers of genes important for any given cell identity.
Conclusions: The extensive mitotic occupancy that we observed is in agreement with a recent study that proposes that TF retention on mitotic chromatin may be a much broader phenomenon than previously appreciated.

Bobbie Pelham-Webb is supported by a Medical Scientist Training Program grant from the National Institute of General Medical Sciences of the NIH under award number T32GM007739 to the Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program. Additionally, this work was funded by the NIH Director s New Innovator Award ( DP2DA043813 ) to Effie Apostolou.

overall_design: Short read signle-end ChIP-seq in V6.5 murine ESC for Klf4 (3 asynchronous and mitotic replicates, respectively ), Oct4 (1 asynchronous replicate with the additional G1 sample of GSE78073, and 2 mitotic replicates with the additional mitotic sample of GSE78073), Sox2(1 asynchronous replicate with the additional asynchronous sample of GSE44288 , and 2 mitotic replicates), H3K27ac (2 asynchronous and mitotic replicates, respectively) and whole cell extract input DNA (7 runs). Mitotic arrest was done as follows: 80-90% confluent mouse ESCs were split 1:3 on gelatinized plates the day before synchronization. Nocodazole at 100ug/ml was added in the medium for 7hr prior to collection by mitotic shake-off.


title: Effect of ZincOxide in Weaned Piglets

status: Public on Apr 19 2017

city: Wageningen

first: Dirkjan

last: Schokker

address: Droevendaalsesteeg 1

department: Wageningen Livestock Research

country: Netherlands

institute: Wageningen UR

summary: Development of immune competence in pigs is important for resilience, disease resistance, and performance later in life. Dietary interventions in early life can contribute to immune system development. Use of model dietary interventions, such as diets with a high concentration of zinc, can contribute to the understanding of the interactions between the diet, the intestinal microbiota and intestinal tissues. The aim of the present study was to evaluate the effects of provision of a diet with a high concentration of zinc (Zn, 2690 mg/kg), as model intervention, as compared to provision of a control diet with a regular Zn concentration (100 mg/kg) during a period of nine days during the post weaning period (d 14-23 post weaning (pw)), on the composition of the intestinal microbiota and gene expression in the intestinal mucosa on d 23 and 35 pw (12 d after the termination of the Zn intervention).    Whole genome gene expression analysis of the jejunal and ileal mucosa revealed a small overall time-treatment interaction effect at d 23 pw in both intestinal tissues. In both jejunal and ileal mucosa various genes/probes were differentially up or down regulated between treatments. In intestinal tissue samples obtained on d 35 no differences in gene expression were observed. Probes of d 23 pw that were differently expressed and had an annotation were subsequently used as input for further functional analysis using DAVID and Gene Decks databases. The analysis did not result in the identification of gene sets that were differentially expressed between dietary treatments. However, it was shown that a number of upregulated genes in the jejunal mucosa on d 23 pw by the high zinc intervention are involved in pathways related to mineral absorption, immune signalling and cell energy metabolism (glycolysis and gluconeogenesis). A few down regulated genes by the Zn intervention are also involved in immune signalling pathways.    It was concluded from the present study that provision of a diet with a high concentration of zinc as zinc oxide during a short period of time (9 days) to piglets in the post weaning period (d 14-23 pw) induces differences on the intestinal expression of genes in part related to the functioning of the local innate immune system. The high dietary zinc intervention can therefore be considered as a suitable model for studying relationships between dietary interventions and development of immune competence in post weaning piglets.

overall_design: In total, 36 piglets were euthanised. i.e.6 pigs per time-point per treatment, 3 time-point; age d42, d51, and d63 (18 pigs), both control and treatment samples (36 pigs)

first: Alfons

last: Jansman

first: Stephanie

last: Vastenhouw


title: Gene expression profile of patients with moderate and severe chronic spontaneous urticaria

city: Barcelona

first: Júlia

last: Perera-Bel


title: Gene expression profile of patients with moderate and severe chronic spontaneous urticaria [tissue]

summary: Chronic spontaneous urticaria (CSU), also traditionally called Chronic Idiopathic Urticaria (CIU), is a common dermatosis. Its estimated point prevalence is 0.6 to 1%. CSU is defined by spontaneously occurring short-lived and itching wheal, angioedema or both. The current nomenclature of urticaria endorses the use of a clinical rather than an aetiological classification to recognise that a percentage of patients with CSU have an autoimmune rather than idiopathic aetiology. As it happens with other IgE-associated diseases, a better knowledge of urticaria patients requires defining phenotypes. The present knowledge about CSU phenotypes is based on the clinical characteristics, associated comorbidities, the course of the disease and its response to the available effective drugs. But a phenotype is defined as the visible characteristics or traits that are a consequence of the expression of genes as well as the influence of environmental factors. The phenotype is part a consequence of the genotype. To study which is the genotype expressed by the patients suffering of CSU can be interesting. The mechanisms involved in the mast cell activation and the role of the released mast cell mediators are well known allowing explaining of how the wheals appear and disappear. But very little is known about the genetic susceptibility and genes involved in the development of wheals in CSU patients. By means of this work, enough case series was collected to draw reliable conclusions, based on the genetic variations found. In order to assess associations between genetic polymorphisms and the different phenotypes of CSU, large case series of well-documented patients with a relevant history are needed. The primary purpose of this study was to identify the most relevant genes expressed in the tissue and the blood samples from patients with moderate and severe CSU.

overall_design:
Objective: The primary purpose of this study was to identify the most relevant genes expressed in the tissue and the blood samples from patients with moderate and severe CSU. The knowledge of the gene profiling differences comparing wheal versus no-lesion skin in selected patients is a real and accurate approach to identify the genes expressed in the wheal developed in patients with CSU.

Patients and methods: A total of 20 patients suffering of moderate and severe CSU/CIU and 10 healthy control subjects were included. The setting of the study was the Department of Dermatology and the Department of Pharmacology Clinic at the Hospital del Mar, Institut Mar d'Investigacions Mediques, Barcelona. The sample size is adequate to the exploratory character of the study. Only patients showing active moderate to severe CSU during at least 3 months were included in the study. Patients were selected prospectively. An Urticaria Activity Score (UAS) 7 defined moderate to severe CSU, this mean an UAS7 ≥16 (UAS 7 range from 0 to 42), where the symptom itch showed a value ≥8. All the patients included remained symptomatic in spite of the treatment with antihistamines. The diagnosis of CSU was based on clinical history data and physical examination. Any active treatment was supplied at the patient at the time where the samples were obtained. Healthy controls were selected from a pool of volunteers. A detailed anamnesis, clinical exploration and basal blood analysis was carried out in order to guarantee that any active disease nor cutaneous nor systemic was present. The CSU patients and the healthy volunteers were submitted to some interventions in order to obtain cutaneous and venous blood samples. Cutaneous biopsies were obtained after local anesthesia using punch biopsy of 4 mm in diameter. Two cutaneous biopsies including skin from an active wheal and one biopsy from non-lesion skin were obtained. The active wheal chosen for biopsy was obtained from the trunk and clinically showed erythema and edema, with a time of evolution of at least of one hour. One of the biopsies taken from the wheal was fixed in formaldehyde and after paraffin inclusion was stained with haematoxilin -eosin, Giemsa and with c-Kit as mast cell marker with the objective to characterize the diagnosis of wheal and describe accurately the characteristics of the inflammatory infiltrate. The second biopsy was immediately prepared for storage prior to be submitted for gene array. Fat and other undesired components that do not belong to the sample were removed before quick-freezing the tissue in liquid nitrogen. Cryopreserved tissue samples were stored at -80°C prior to the gene microarray study. The punch taken over no-lesion skin guarantee that no wheal was present in the previous 72 hours and no other skin alteration was present i.e., desquamation or pigmentation. Venous blood analysis was obtained from the basilic mediana vein in the antecubital fossae and prepared for its storage for gene array analysis. Quality control of RNA samples was performed with the Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA). Good quality samples with an RNA Integrity Number (RIN) value >6, and also some mildly degraded samples with a RIN value between 4 and 6, were processed following specific protocols. The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Based on the results provided from the microarray comparative analysis, we selected a set of genes to be confirmed by Q-PCR. The criteria followed to perform such selection were based in technical aspects that would guarantee gene confirmation. These recommendations include an adjusted P value of 0.05 and a Log fold change of 1 (plus or minor to 1). The second criteria was based in an accurate analysis of the genes up or down regulated and its possible involvement in mast cell biology, wheal pathogenesis, urticaria or allergy. The data base included shows the raw data of the gene-array performed in the available samples of the blood and the tissue of the patients with CSU and the healthy controls included in this study.

61 samples were analyzed from 30 individuals, 20 patients and 10 healthy controls. This Series includes the samples from tissue.

first: Ana

last: Giménez-Arnau


title: Gene expression profile of patients with moderate and severe chronic spontaneous urticaria [blood]

overall_design:
Objective: The primary purpose of this study was to identify the most relevant genes expressed in the tissue and the blood samples from patients with moderate and severe CSU. The knowledge of the gene profiling differences comparing wheal versus no-lesion skin in selected patients is a real and accurate approach to identify the genes expressed in the wheal developed in patients with CSU.

Patients and methods: A total of 20 patients suffering of moderate and severe CSU/CIU and 10 healthy control subjects were included. The setting of the study was the Department of Dermatology and the Department of Pharmacology Clinic at the Hospital del Mar, Institut Mar d'Investigacions Mediques, Barcelona. The sample size is adequate to the exploratory character of the study. Only patients showing active moderate to severe CSU during at least 3 months were included in the study. Patients were selected prospectively. An Urticaria Activity Score (UAS) 7 defined moderate to severe CSU, this mean an UAS7 ≥16 (UAS 7 range from 0 to 42), where the symptom itch showed a value ≥8. All the patients included remained symptomatic in spite of the treatment with antihistamines. The diagnosis of CSU was based on clinical history data and physical examination. Any active treatment was supplied at the patient at the time where the samples were obtained. Healthy controls were selected from a pool of volunteers. A detailed anamnesis, clinical exploration and basal blood analysis was carried out in order to guarantee that any active disease nor cutaneous nor systemic was present. The CSU patients and the healthy volunteers were submitted to some interventions in order to obtain cutaneous and venous blood samples. Cutaneous biopsies were obtained after local anesthesia using punch biopsy of 4 mm in diameter. Two cutaneous biopsies including skin from an active wheal and one biopsy from non-lesion skin were obtained. The active wheal chosen for biopsy was obtained from the trunk and clinically showed erythema and edema, with a time of evolution of at least of one hour. One of the biopsies taken from the wheal was fixed in formaldehyde and after paraffin inclusion was stained with haematoxilin -eosin, Giemsa and with c-Kit as mast cell marker with the objective to characterize the diagnosis of wheal and describe accurately the characteristics of the inflammatory infiltrate. The second biopsy was immediately prepared for storage prior to be submitted for gene array. Fat and other undesired components that do not belong to the sample were removed before quick-freezing the tissue in liquid nitrogen. Cryopreserved tissue samples were stored at -80°C prior to the gene microarray study. The punch taken over no-lesion skin guarantee that no wheal was present in the previous 72 hours and no other skin alteration was present i.e., desquamation or pigmentation. Venous blood analysis was obtained from the basilic mediana vein in the antecubital fossae and prepared for its storage for gene array analysis. Quality control of RNA samples was performed with the Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA). Good quality samples with an RNA Integrity Number (RIN) value >6, and also some mildly degraded samples with a RIN value between 4 and 6, were processed following specific protocols. The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Based on the results provided from the microarray comparative analysis, we selected a set of genes to be confirmed by Q-PCR. The criteria followed to perform such selection were based in technical aspects that would guarantee gene confirmation. These recommendations include an adjusted P value of 0.05 and a Log fold change of 1 (plus or minor to 1). The second criteria was based in an accurate analysis of the genes up or down regulated and its possible involvement in mast cell biology, wheal pathogenesis, urticaria or allergy. The data base included shows the raw data of the gene-array performed in the available samples of the blood and the tissue of the patients with CSU and the healthy controls included in this study.

61 samples were analyzed from 30 individuals, 20 patients and 10 healthy controls. This Series includes the samples from blood.