title: Analyses of phyB-regulated genes by RNA-seq

status: Public on Jul 25 2020

city: Shanghai

first: weiwei

last: Qi

address: No 99 Shangda Road

institute: Shanghai  University

summary: The phytochrome family consists of five numbers (phyA-phyE) in Arabidopsis, of which phyB is the best characterized and shown to play a major role in mediating red light inhibition of hypocotyl elongation. In order to reveal the molecular basis for phyB-mediated red light signaling to promote photomorphogenesis, we analyzed the gene expression profile of red light-grown WT and phyB mutant seedlings by high throughput sequencing.

overall_design: WT and phyB mutant seedlings were grown on 1/2 MS plates plus 1% sucrose under 60 μmol m-2 s-1 red light for 4.5 days. mRNA from each samples was sequenced to analyze the genes regulated by phyB.

first: Feng

last: Xu

first: Hong-quan

last: Yang


title: Human dendritic cell and macrophage response to SARS-CoV-2 infection

city: St. Louis

first: Siyuan

last: Ding

state: MO

address: 425 S. Euclid Ave., MPRB, Rm 9220

department: Molecular Microbiology

country: USA

institute: Washington University in St. Louis

type: Expression profiling by high throughput sequencing

summary: The goal of this study is to use RNA-sequencing to profile the transcriptional changes in human PBMC derived dendritic cells and macrophages upon SARS-CoV-2 infection. Specifically, we are interested in determining the cytokine and chemokine up-regulation in response to SARS-CoV-2 infection at 2 hours post infection since cytokine storms were observed in severe COVID-19 patients. Multiple chemokines including IL-6 and CXCL10 were up-regulated by SARS-CoV-2 infection in both dendritic cells and macrophages, implying a potential detrimental effect of myeloid cells in exacerbating immunopathology of COVID-19 diseases.

overall_design: mRNA profiles of mock and SARS-CoV-2 infected human dendritic cells and macrophages were analyzed by bulk RNA-sequencing

first: M

middle: F

last: Gomez Castro

first: S


title: Dissecting the Genetic Architecture of Renal Function and the biomarker Cystatin C in Aging

status: Public on Jul 27 2020

city: Davis

first: Brian

middle: J

last: Bennett

state: CA

address: 430 West Health Sciences Drive

department: Obesity and Metabolism

institute: Western Human Nutrition Research Center, ARS

summary: In this study, we utilized 95 Diversity Outbred (DO) female mice, 56 weeks of age, to perform eQTL analysis of renal biomarkers in blood and urine. We also determined the correlation between kidney biomarkers and expression levels of the genes in kidney.

overall_design: Female Diversity Outbred mice (n = 120; J: DO; G16; JAX stock number 009376) were obtained from the Jackson Laboratory (Bar Harbor, ME) at 4 weeks of age. The mice were group housed (n = 5 mice per cage) and maintained on chow diets. At about 56 weeks of age, mice were injected intraperitoneally with a volume of sterile isotonic saline equivalent to 10 percent of their body weight and on the following day mice were fasted for 4 hours, anesthetized, and dissected to kidney samples for micro array analysis. Microarray data were available from 95 kidney samples

middle: N

last: Huda


title: Pancreatic endocrine tumour (PET)_Affymetrix 500K SNP arrays

city: London

first: Tomohiko

last: Harada

address: Charterhouse Square

department: Centre for Molecular Oncology

country: United Kingdom

institute: Cancer Research UK

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary:
To identify genetic alterations involved in the pathogenesis of PETs, we have analysed a total of 32 PET samples (29 tissue specimens and 3 cell lines) using high-resolution single nucleotide polymorphism (SNP) arrays.

Keywords: comparative genomic hybridisation

overall_design: A total of 29 fresh-frozen PET tissue specimens (all from primary lesions) were obtained surgically in University of Verona, Italy, with ethical approval of the institutions under the Helsinki Declaration. All tumour tissues were diagnosed histologically by a pathologist and confirmed to be occupied with at least 70% of neoplastic cells before involved in this study. Normal pancreatic tissues were available in 20 out of 29 PET samples and used as a reference. Three human PET cell lines (CM; metastatic insulinoma, BON; metastatic carcinoid, QGP-1; somatostatinoma) were also acquired from University of Verona, Italy. Tumour and reference genomic DNAs were extracted using Qiagen DNA extraction kit (Qiagen Ltd., Sussex, UK).

first: Claude

last: Chelala

first: Davide

last: Antonello

first: Stefano

last: Barbi

first: Stefania

last: Beghelli

first: Tatjana

last: Crnogorac-Jurcevic

first: Aldo

last: Scarpa

first: Nicholas

middle: R

last: Lemoine


title: Analyses of red light-regulated genes by RNA-seq

country: China

summary: Light, as both energy source and informational signal, profoundly influences plant growth and development during the whole life span from seed germination to flowering. To dissect the role for red light signaling in regulate the seedling development, we analyzed the gene expression profile of red light- and dark-grown WT seedlings by high throughput sequencing.

overall_design: WT seedlings were grown on 1/2 MS plates plus 1% sucrose under dark and 60 μmol m-2 s-1 red light. mRNA from each samples was sequenced to analyze the genes regulated by red light signaling.


title: Comparison of expression profiles for Nicotiana benthamiana agroinfiltrated with caryophyllene synthase and SNARE-RNAi

city: Wageningen

first: Hieng-Ming

last: Ting

state: Gelderland

address: Droevendaalsesteeg 1

department: Laboratory of Plant Physiology

country: Netherlands

institute: Wageningen University

summary: Here we show for the first time that vesicle fusion is one of multiple pathways in plant cells involved in terpene emissions. We demonstrate a positive feedback on terpene production when vesicle fusion is inhibited in cells producing high levels of terpenes, which relates to an induced proteasome malfunction.

overall_design: N. benthamiana leaves were infiltrated with Agrobacterium containing the following expression constructs: (1) pBin+DsRed-RNAi, (2) MtVAMP721e-RNAi+DsRed-RNAi, (3) CST+DsRed-RNAi, (4) CST+MtVAMP721e-RNAi (six plants per construct, one leaf per plant). Infiltrated leaves were harvested seven days post agroinfiltration. Per sample two leaves were pooled, resulting in three biological replicates for each treatment. Followed by deep sequencing,  using Illumina Hiseq 2000.

first: Alexander

last: van der Krol


title: RNA-Seq timeseries of Adventitious root development in Populus ussuriensis

status: Public on Jul 24 2020

city: Harbin City

first: Chenghao

last: Li

state: HeiLongJiang Province

address: No. 51 HeXing Road,Xiangfang District

department: College of Forestry

institute: Northeast Forestry University

summary: For the RNA-seq experiments two week-old seedlings were cutting and subsequently transfer to 1/2 MS medium with or without 1 μM MeJA at 2 time points over a 1-h period and harvested the basal ends of stem cuttings (0.5 cm). Samples were collected from two biological replicates (40 cuttings each).

overall_design: RNA-seq of the basal ends of stem cuttings (0.5 cm)

first: Hairong

last: Wei

first: Quangang

last: Liu

first: Wenlong


title: Bulk mRNA sequencing of wildtype (WT) and mutator mouse embryonic fibroblasts (MEFs)

status: Public on Jul 26 2020

city: Biberach

first: Meshal

last: Ansari

address: Birkendorfer Straße 65

country: Germany

institute: Boehringer Ingelheim

summary: The proteasome is the main proteolytic system for targeted protein degradation in the cell. Its function is fine-tuned according to cellular needs. Inhibition of the respiratory chain impairs proteasome activity, regulation of proteasome function by mitochondrial metabolism, however, is unknown.   Here, we demonstrate that mitochondrial dysfunction reduces the assembly and activity of the 26S proteasome. Defects in respiratory chain caused metabolic reprogramming of the Krebs cycle and deficiency in the amino acid aspartate resulting in reduced 26S proteasome function. Aspartate supplementation fully restored assembly and activity of 26S proteasome complexes. This metabolic reprogramming involved sensing of aspartate via the mTORC1 pathway and the mTORC1-dependent transcriptional activation of defined proteasome assembly factors. Metabolic regulation of 26S function was confirmed in patient-derived skin fibroblasts with respiratory dysfunction containing a single mitochondrial mutation. Importantly, treatment of primary human lung fibroblasts with the respiratory chain inhibitor and anti-diabetic drug metformin similarly reduced assembly and activity of 26S proteasome complexes, which was fully reversible and rescued by supplementation of aspartate or pyruvate. Of note, reduced 26S activity conferred increased resistance towards the proteasome inhibitor Bortezomib, which was reversible upon pyruvate supplementation.  Our study uncovers a fundamental novel mechanism of how mitochondrial metabolism adaptively adjusts protein degradation by the proteasome. It thus unravels unexpected consequences of defective mitochondrial metabolism in disease or drug-targeted mitochondrial reprogramming for proteasomal protein degradation in the cell. As metabolic inhibition of proteasome function can be alleviated by treatment with aspartate or pyruvate, our results also have therapeutic implications.

overall_design: Bulk mRNA from WT (4 technical replicates) and mutator (5 technical replicates) MEFs was sequenced to analyze expression of proteasome subunits

first: Thomas

last: Meul

first: Elisabeth

last: Graf

last: Schwarzmayr


title: Characterization of lncRNA and mRNA Profiles in Rats With Diabetic Macroangiopathy

city: Chengdu

first: chan

last: yang

address: No 39 Shi-er-qiao Road

institute: Hospital of Chengdu University of Traditional Chinese Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Diabetic macroangiopathy is one of the most common serious complications of diabetes. Previous studies indicate that lncRNAs involved in the process of diabetes and another vascular disease. However, their detailed mechanism of the lncRNAs involved in diabetic macroangiopathy has not been well characterized. In the present study, we generated rat models of diabetic macroangiopathy induced by High fat. A total of 15 GK rats was constructed as a test group, along with 15 Wistar rats set as a control group, and thoracic aorta tissue from each group was collected. Whole genomic RNA sequencing was performed on thoracic aorta tissue;3223 novel lncRNAs and 20367 annotated lncRNAs were identified in thoracic aorta samples, and 864 lncRNAs were expressed differently in the test and control groups. Gene ontology term enrichment showed the apparent enrichment of inflammatory response and cell apoptosis, which consistent with the results of H&E Staining, TUNEL Assay, and ELISA; Extensive literature reveals inflammatory response and cell apoptosis play an important role in the process of diabetic macroangiopathy.The results of the present study indicated that lncRNAs, especiallyNrep.bSep08,Col5a1,aSep0,soygee.aSep08-unspliced,NONRATT013247.2,votar.aSep08-unspliced,etc,both participate in and mediate the process of inflammatory response,cell apoptosis.What’s more, Our research provides further insights into the understanding of the basic molecular mechanisms underlying diabetic macroangiopathy.

overall_design: Our research showed that characterization of lncRNA and mRNA Profiles in Rats With Diabetic Macroangiopathy by High-throughput sequencing technology which was used to obtain the differential mRNA/lncRNA expression profiles of the thoracic aorta of each group of rats, further screen the differential mRNA/differential lncRNA target gene collection, and use GO enrichment and KEGG enrichment for biological analysis. Interpret the characterization of lncRNA and mRNA Profiles in Rats With Diabetic Macroangiopathy from the molecular level.


title: Antisense RNA-mediated photosynthetic response in Synechocystis sp. PCC6803

city: Daejeon

first: Byung-Kwan

last: Cho

address: 291 Daehak-ro

country: South Korea

institute: KAIST

summary: Antisense RNAs (asRNAs) have diverse functions across three superkingdoms of life. However, their physiological roles for photosynthesis, the most efficient conversion system of solar energy and carbon dioxide into desirable biofuel, are elusive. To understand asRNA-mediated photosynthetic response, we systematically identified non-coding asRNAs and analyzed their differential regulation upon high light and/or low temperature. We found that large fractions of antisense regions are pervasively transcribed and differentially induced upon the change of light and/or temperature. Particularly, photosynthesis and ribosome related genes are mostly regulated by asRNA. Futhermore, we found that 93 long non-coding asRNAs spanning more than half of the cognate open reading frames (ORFs), unexpectedly. Intriguingly, many of them are associated with photosynthetic genes and they have positive role to the expression level of their cognate ORFs. Thus, our systematic transcriptome analysis of photosynthetic response indicates that asRNAs may finetune transcriptional response to enable efficient photosynthetic energy conversion.

overall_design: Directional RNA-seq (ScriptSeqTM) of high light stress and/or low temperature stress were generated in duplicates by using Illumina MiSeq

first: Yoo-Bok

first: Seong-Joo

last: Hong

first: Hyojin

last: Kim

first: Borahm

last: Lee

first: Suhyung

first: Hyeonseok

last: Shin

first: Jin-Woo

first: Hyung-Kyoon

last: Choi

first: Choul-Gyun

first: Hookeun


title: In vivo isolated Wnt1-Prim1 Primary, Residual, and Recurrent Tumor Cells

city: Philadelphia

first: Lewis

last: Chodosh

state: Pennsylvania

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

summary: Residual disease represents a major obstacle to the successful treatment of breast cancer, however little is known about the biology of residual tumor cells in vivo.  To identify genes differentially expressed in vivo in residual tumor cells compared to primary tumor cells or recurrent tumor cells, we used flow cytometry to isolate GFP-labeled tumor cells from primary, residual, or recurrent tumors grown orthotopically in nu/nu mice. WTA was used to amplify RNA from all tumor cells.

overall_design: Three timepoints (Primary tumor, residual disease, recurrent tumor) were taken with 3-4 replicates per timepoint.

first: Dhruv

middle: K

last: Pant

first: Jason

last: Ruth

middle: A


title: Inhibiting MYC-regulated Glutaminase Metabolic Axis is an Effective Synthetic Lethal Approach for Treating Chemoresistant Cancers

status: Public on Jul 23 2020

city: Baltimore

first: Tian-Li

last: Wang

state: MD

address: 1551 Jefferson st.

department: Department of Pathology, Oncology, and Gynecology/Obstetrics

institute: Johns Hopkins University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Amplification and expression of the MYC oncogene in tumor cells, including ovarian cancer cells correlates with poor responses to chemotherapy. As MYC is not directly targetable, we have analyzed molecular pathways downstream of MYC to identify potential therapeutic targets. We have discovered that ovarian cancer cells overexpressing glutaminase (GLS), a MYC target and  a key enzyme in glutaminolysis, are intrinsically resistant to platinum chemotherapy, and are enriched in the intracellular antioxidant glutathione. Deprivation of glutamine by glutamine-withdrawal, GLS knockdown, or exposure to the GLS inhibitor CB-839 resulted in robust induction of reactive oxygen species in high GLS-expressing but not low GLS-expressing ovarian cancer cells. Treatment with CB-839 rendered GLShigh 10 cells vulnerable to the poly(ADP-ribose) polymerase (PARP) inhibitor, olaparib, and prolonged survival in tumor-bearing mice. Our findings suggest that applying a combined therapy of GLS inhibitor and PARP inhibitor could effectively treat chemoresistant ovarian cancers, especially those with high GLS expression.

overall_design: MYC ChIP-seq experiments in two human cancer cell lines. ChIP-seq library preparation and sequencing were performed by NextSeq500 platform.

first: Yao-An

last: Shen

first: Fang-Chi

last: Hsu

first: Yohan

middle: S

last: Rahmanto

first: Jin

last: Jung

first: Xi

last: Chen


title: Thrombopoietic Agents: Novel Osteoinductive Agents for Bone Healing

city: Fredrick

first: Nabarun

last: Chakraborty

address: 568 Doughten Dr

institute: WRAIR

summary: Achieving bone union remains a significant clinical dilemma. The use of osteoinductive agents, specifically BMPs , has gained wide appreciable attention. However, multiple side effects, including increased incidence of cancer, has renewed interest in investigating other alternatives that provide safer, yet effective bone regeneration. Here we demonstrate the robust bone healing capabilities of the main megakaryocyte growth factor, thrombopoietin (TPO) and/or second generation TPO agents in mice, rats, and pigs. This bone healing activity is shown in two fracture models (critical sized defect or CSD and closed fracture) and with local or systemic administration.  Our transcriptomic analyses, cellular studies, and protein arrays demonstrate that TPO enhances angiogenesis, an important aspect of successful bone repair. Finally, the therapeutic potential of thrombopoietic agents is high since they are used in the clinic for other indications (e.g. thrombocytopenia).

overall_design: n=12,  3 treatments (Saline, BMP-2 and TPO)  and 4 replicates of each treatment


title: RNase and sRNA activity in Brucella abortus

city: Blacksburg

first: Robert

last: Settlage

state: VA

address: 1 Washington St

department: Advanced Research Computing

institute: Virginia Tech

summary: Isogenic deletion and truncation of specific genes encoding RNases in Brucella abortus were analyzed for changes in gene expression. The main goal of this work is to determine the mRNAs that exhibit dysregulation when small regulatory RNAs (i.e., Bsr8) or RNases (i.e., RNaseE and RNaseJ) are invactivated in Brucella abortus. Small regulatory RNAs often control gene expression by binding directly to mRNAs to block translation or induce their degradation, and RNA from a deletion of one sRNA gene, bsr8, was analyzed to uncover the mRNAs that may be controlled by BsrB. RNases are enzymes that cleave RNAs during processing, turnover, and regulatory events, and RNaseE and RNaseJ appear to be important for B. abortus virulence. Therefore, to determine the mRNAs potentially targetd by these RNases, RNA from a strain harboring a RNaseE truncation and a strain carrying a deletion of rnaseJ were analyzed. In the end, the objective of this study was to gain insight into the regulatory patterns of specific B. abortus sRNAs and RNases.

overall_design:
Isogenic deletion and truncation of specific genes encoding RNases in Brucella abortus were analyzed for changes in gene expression.
Biological triplicate samples were used for each strain.

first: Clayton

middle: C

last: Caswell

first: Lauren

middle: M

last: Sheehan

first: James

last: Budnick

first: Jaquille

last: Fyffe-Blair

first: Kellie

last: King

middle: E


title: Expression data from human AML cell lines

city: Bologna

first: Annalisa

last: Lonetti

address: Via Massarenti, 11

department: “Giorgio Prodi” Interdepartmental Cancer Research Centre

country: Italy

institute: University of Bologna

summary: Pediatric Acute Myeloid Leukemia (AML) is an aggressive and poor prognosis malignancy for which there are few effective targeted approaches, despite the numerous genetic alterations, including MLL gene rearrangements (MLL-r). The histone methyltransferase DOT1L is involved in supporting proliferation of MLL-r cells, for which a target inhibitor, Pinometostat, has been evaluated in a clinical trial recruiting pediatric MLL-r leukemic patients. However, modest clinical effects have been reported. Recent studies reported that additional leukemia subtypes lacking MLL-r are sensitive to DOT1L inhibition. Here we report that targeting DOT1L with Pinometostat sensitizes pediatric AML cells to further treatment with the multi-kinase inhibitor Sorafenib, irrespectively of MLL-r. DOT1L pharmacologic inhibition induces AML cell differentiation and modulated expression of genes with relevant roles in cancer development. Such modifications in transcriptional program impact on further treatments, inducing a strong sensitization to Sorafenib, with increased apoptosis and growth suppression of both AML cell lines and primary pediatric AML cells with diverse genotypes. We used microarrays to define differential regulation of gene expression in AML cell lines with or without MLL gene rearrangements following pharmacologic inhibition of DOT1L.

overall_design: We analyzed duplicates of 7 AML cell lines, including 4 MLL-r cell lines (MV4-11, MOLM-13, NOMO-1, THP-1) and 3 non MLL-r cell lines (OCI-AML-3, U-937, HL-60) treated with vehicle (0.01% DMSO) as control cells or treated with 1 µM Pinometostat for 8 days.

first: Maria

last: Laginestra

first: Valentina

last: Indio


title: Bulk RNA-seq of aorta intima resident macrophage from B6, and adventitia macrophages from ApoE-/- mice

first: Maxim

last: Artyomov

state: Missouri

address: 425 S Euclid Ave

department: Pathology & Immunology

institute: WASHINGTON UNIVERSITY IN ST LOUIS

summary: Macrophages in atherosclerotic aorta are major population in lesion and contributes to lesion formation by becoming foam cells. To investigate in determine diversity of arterial macrophage, we extracted aorta intima resident macrophages (CD11c+ MHC II+ CD64+ macrophages from C57BL/6 mice, as well as adventitia macrophages from atherosclerotic aorta (which complement our prior submissions of foamy and non-foamy intima macrophage). Our data identify unique gene expression signatures for these different macrophage populations in the aorta.

overall_design: C57BL/6 samples were derived from 5-mice  pooled for each sample. Adventitia macrophage samples from ApoE-/- mice (n=6) were fed high fat diet for 28 weeks prior to sacrifice. Samples were sorted on a BD Aria III and sequenced by Illumina HiSeq-3000.

first: Jesse

middle: W

last: Williams

first: Konstantin

last: Zaitsev

first: Ki-Wook

last: Kim

first: Stoyan

last: Ivanov

first: Brian

last: Saunders

first: Patricia

last: Schrank

first: Kyeondae

first: Andrew

last: Elvington

first: Seung

middle: H

first: Christopher

middle: G

last: Tucker

first: Mary

last: Wohltmann

middle: T

last: Fife

first: Slava

last: Epelman

first: Kory

last: Lavine

first: Bernd

last: Zinselmeyer

first: Jae-Hoon

last: Choi

first: Gwendalyn

last: Randolph


title: Histone mark and Mediator1 ChIP-seq in human cell lines

first: Kathrin

last: Bernt

state: PA

address: 3501 Civic Center Boulevard,

institute: Children's Hospital of philadelphia

summary: We show that translocations place regulatory regions in close proximity to MN1 and enhance gene expression

overall_design: ChIP-seq of H3K27ac, H3K4me1, and Mediator1 in two human AML cell lines with MN1-ETV6 translocation and two control cell lines

first: Simone

last: Riedel

first: Hongbo

last: Xie


title: REST ChIP-seq in human and mouse hippocampus

city: Portland

first: James

middle: Christopher

last: McGann

state: Oregon

address: 3181 SW Sam Jackson Park Road

department: Vollum Institute

institute: Oregon Health and Science University

summary: The transcriptional repressor REST (RE1 Silencing Transcription Factor) is a master regulator of thousands of neuronal genes that together impart the terminally differentiated neuronal phenotype. Because of this unique feature, REST has been, and continues to be, a widely used model for understanding neurogenesis and neuronal cell function. These studies have focused primarily on murine embryonic development, but recent studies have pointed to distinct postnatal roles for REST in stroke, epilepsy, aging and cognitive decline. The function of REST in healthy human brain tissue, however, still remains poorly characterized. Here, we present deep sequencing chromatin immunoprecipitation evidence for divergent REST function in normal mouse and human postmortem adult hippocampus. In mouse, REST occupies only 221 peaks that are divided between prototypical REST target genes shared with non-neuronal cells, as well as peaks unique to the hippocampus. Surprisingly, the mouse hippocampal-unique sites are not conserved in human, which contains 1886 REST peaks unique to the hippocampus. Further, the REST peaks unique to the hippocampus represent a potentially new category of target genes encoding proteins important in the immune response. Our results suggest the possibility that REST protects against aberrant immunological responses during normal human aging and that mouse may not model this aging function.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of REST-bound regions in post-mertem tissue from human and mouse hippocampus

first: Saurabh

last: Garg

first: Randall

last: Woltjer

first: Gail

last: Mandel


summary: Transcriptional effects of MN1 polyQ-stretch deletion in murine HSPCs

overall_design: RNA-seq of murine HSPCs overexpressing MN1 or MN1-∆pQ. Three independent samples for MN1 overexpression, three independent samples for MN1-∆pQ, and one untransduced sample (noTD)

first: Xie

last: Hongbo


title: Gene expression profiling of Lentivirus-mediated Gene Silencing of RARβ Inhibits A549 Non-Small Cell Lung Cancer stem cells

city: Kepala Batas

first: Badrul

middle: Hisham

last: Yahaya

state: Penang

address: Bertam, Kepala Batas

department: Advanced Medical & Dental Institute

country: Malaysia

institute: Advanced Medical and Dental Institute

summary:
Retinoic acid Receptor Beta (RARβ) protein encoded by RARβ gene is a nuclear receptor protein that binds to retinoic acid (RA) to mediate RA function in cellular signalling in embryogenic morphogenesis, cell growth and differentiation. However, the function of RARβ in cancer stem cells (CSCs) maintenance of non-small cell lung cancer (NSCLC) is yet to be determined
We used microarrays to analyse the trancriptomic changes in lung cancer and cancer stem cells following RARβ silencing.

overall_design: Lentivirus-mediated RARβ downregulation using ShRNA was performed in A549 cells, A549 putative CSCs (CD166+EpCAM+ and CD166+CD44+) and putative non-CSCs (CD166-EpCAM- and CD166-CD44-). Total RNA was extracted and hybridize on Affymetrix microarrays. We sought to obtain homogeneous populations of embryos at each developmental stage in order to increase the temporal resolution of expression profiles. To that end, we hand-selected embryos according to morphological criteria at five time-points: before pole cell formation, i.e. before zygotic transcription (T0), during the slow phase (T1) and the fast phase (T2) of cellularisation and at the beginning (T3) and the end (T4) of gastrulation.

first: Noor

last: Abu Halim

first: Norashikin

last: Zakaria


city: Haikou

first: Pingjuan

last: Zhao

address: XueYuan Road 4

department: Institute of Tropical Bioscience and Biotechnology

institute: Chinese Academy of Tropical Agricultural Sciences

summary:
Transcriptome  Analysis of Wild Type and Histone H1.2(MeH1.2) Transgenic Plants  by RNA-seq in Cassava.The goal of this study was to compare the phenotypic and transcriptome differences between transgenic and WT plants, and to analyze how overexpression of MeH1.2 gene changed the expression patterns.
MeH1.2 overexpressed transgenic cassava plant (HOE) were was made. The 2-month-old seedlings of HOE were significantly smaller and weaker than of the wild type (WT) under Murashige and Skoog (MS) medium, while, the leave leaf became yellow senescence and the number of branch root increased significantly in HOE than in WT. We found a total of 1670 down-regulated differentially expressed genes (DEGs) and 891 up-regulated DEGs in HOE leave of 2-months-old bottled seedling as indicated by RNA-seq. Many of DEGs were associated with growth metabolism and stress response, such as different amino acids metabolic genes, wound-responsive family genes and peroxidase superfamily genes. We hypothesized the overexpression of MeH1.2 may be similar to mild abiotic stress to retard the growth of HOE, the increased proline content and root-shoot ratio of HOE also support the hypothesis.

overall_design: mRNA profiles of 2-month-old wild type (WT) and MeH1.2 overexpressed transgenic cassava plant

first: Xin

last: Guo

first: Bin

last: Wang


title: The stem cell pluripotency genes Klf4 and Oct4 regulate complex SMC phenotypic changes critical in late-stage atherosclerotic lesion pathogenesis

city: Charlottesville

first: Gary

last: Owens

address: 415 Lane Road MR5 Building Room 1322

institute: University of Virginia

summary: Background Rupture or erosion of advanced atherosclerotic lesions with a resultant myocardial infarction or stroke are the leading worldwide cause of death. However, we have a very limited understanding of the identity, origin, and function of many cells that make up late stage atherosclerotic lesions, as well as the mechanisms by which they control plaque stability. Methods and Results Using RNAseq and ChIPseq of advanced atherosclerotic lesions from mice, we provide evidence SMC-specific Klf4- versus Oct4-knockout ApoE-/- mice showed virtually opposite genomic signatures and putative SMC Klf4 or Oct4 target genes play an important role regulating SMC phenotypic changes.  Further, we conducted a comprehensive single-cell RNA-seq of advanced human carotid endarterectomy samples and compared these with scRNAseq from murine micro-dissected advanced atherosclerotic lesions with SMC and endothelial lineage tracing to survey all plaque cell types and rigorously determine their origin. This analysis revealed remarkable similarity of transcriptomic clusters between mouse and human lesions and extensive plasticity of SMC- and EC-derived lesion cells. The latter included 7 distinct clusters of SMC- and EC-derived cells, most negative for traditional markers. In particular, SMC contributed to a Myh11-, Lgals3+ population with a chondrocyte-like gene signature that was markedly reduced with SMC-specific conditional knockout of Klf4. To study these cells and the mechanisms of their transition, we developed an innovative dual lineage tracing mouse that can uniquely label and genetically target Myh11+ SMC that subsequently activate Lgals3. We observed that SMC that activate Lgals3 comprise up to 2/3 of all SMC in advanced plaques. However, initial activation of Lgals3 in these cells does not represent conversion to a terminally differentiated state, but rather represents transition of these cells to a unique stem cell marker gene+, ECM-remodeling, “pioneer” cell phenotype that are the first to invest within lesions and subsequently give rise to at least 3 other SMC phenotypes within advanced lesions including Klf4-dependent osteogenic phenotypes likely to contribute to plaque calcification and plaque destabilization. Conclusions Taken together, these results provide evidence that SMC-derived cells within advanced mouse and human atherosclerotic lesions exhibit far greater phenotypic plasticity than generally believed, with Klf4 regulating transition to multiple phenotypes including Lgals3+ osteogenic cells likely to be detrimental for late stage atherosclerosis plaque pathogenesis.

overall_design: ChIP-seq of Oct4 and scRNA-seq of atherosclerotic plaques of Apoe-/- mouse (with or without specific Klf4 KO) and in human samples

first: Gabriel

last: Alencar

first: Katherine

last: Owsiany

first: Santosh

last: Karnewar

first: Katyayani

last: Sukhavasi

first: Giuseppe

last: Mocci

first: Anh

last: Nguyen

first: Corey

last: Williams

first: Sohel

last: Shamsuzzaman

first: Michal

last: Morky

first: Chris

last: Henderson

first: Ryan

last: Haskins

first: Richard

last: Bailys

first: Aloke

middle: V

last: Finn

first: Coleen

last: McNamara

first: Eli

last: Zunder

first: Vamsidhar

last: Venkata

first: Gerard

last: Pasterkamp

first: Johan

last: Björkegren

first: Stefan

last: Bekiranv


title: Expression data of ex vivo purified CD4+ cells from WT and P2rx7-/- mice

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

summary:
Extracellular adenosine triphosphate (eATP) is a signaling molecule that affects T cell function via the ionotropic P2X7 receptor. The study of effector/memory T cells isolated from mice with deletion of P2rx7, the gene encoding for P2X7, allowed understanding the impact of P2X7 activity on T cell function in the eATP-rich tumor microenvironment.
To explore the the transcriptional impact of the lack of P2rx7 in CD4+ naïve and TEM cells, we performed genome-wide expression profiling of ex vivo purified CD4+ naïve and TEM cells from WT and P2rx7-/- mice

overall_design: CD4+ naïve and TEM cells were isolated from secondary lymphoid organs of WT and P2rx7-/- mice. Gene expression profiling was performed to identify transcripts modulated by eATP via P2X7 that coud affect the anti-tumor adaptive immune response.

first: Fabio

last: Grassi

first: Andrea

last: Romagnani

first: Elsa

last: Rottoli


title: Single-cell epigenomics identifies a premetastatic regulatory program in lung adenocarcinoma [scATAC-seq]

city: Cambridge

first: Lindsay

last: LaFave

state: MA

address: 77 Massachusetts Avenue; 76-453

department: Biology

institute: MIT

summary: Here we use an improved single-cell chromatin profiling approach to determine epigenomic alterations across tumor progression in a mouse model of lung adenocarcinoma (LUAD). Specifically, we induced tumors by providing Adeno-SPC-Cre virus to mice intratracheally to induce tumors due to conditional expression the Kras G12D mutation and loss of p53 (termed the KPT model). Mice also expressed a tdTomato reporter allele allowing for the sorting of tumor cells in late-stages of tumor progression. Using a combinatorial indexing approach (sciATAC-seq), we identify an epigenomic continuum representing a loss of cellular identity and progression towards a metastatic state.

overall_design: Biorad droplet based scATAC-seq on tumor-burdened lung from 8 week time point. Sorted tdTom positive tumor cells were profiled for chromatin accessibility changes.

first: Vinay

last: Kartha

first: Sai

last: Ma


title: Lipopolysaccharide-dependent transcriptional regulation of PU.1 in microglial cells

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

institute: Hanyang Univ.

summary: We knocked out PU.1 in murine BV-2 cells using the CRISPR-Cas9 system to investigate the role of PU.1 in the expression of immune-related genes. RNA sequencing and subsequent bioinformatic analysis revealed that the expression of most of the immune-related genes was suppressed in the absence of PU.1

overall_design: Examination of effects of LPS-stimulated BV2-PU.1-KO-cells, were generated by deep sequencing on an Illumina HiSeq 2000 (101 cycles PE lane).

first: Young


title: Next Generation Sequencing Facilitates Quantitative Analysis of ADORA1 knockdown and scrambled-shRNA control cells' Transcriptomes

city: Shanghai

first: Youqiong

last: Ye

address: 280 Chongqing south road

institute: Shanghai Jiao Tong University School of Medicine

summary: Expression profiles of ADORA1-shRNA-transfected Sk-mel-28 human melanoma cell line and scrambled-shRNA control cells

overall_design: Expression profiles were generated from ADORA1-shRNA-transfected Sk-mel-28 human melanoma cell lines, which were collected to extract total RNA, and mRNA sequencing was performed.

first: Hong

last: Liu

first: Xinwei

last: Kuang


title: Tumor cells that survive oncogenic pathway inhibition exhibit cellular dormancy

first: Lewis

last: Chodosh

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

overall_design: Refer to individual Series


title: Transcriptional dissection by single-cell RNASeq analysis of the metastasis settings from a highly metastatic Patient-Derived Xenograft model of pancreatic ductal adenocarcinoma

city: Heidelberg

first: Javier

last: Perales-Paton

state: Baden-Württemberg

address: Im Neuenheimer Feld 267

department: Faculty of Medicine

institute: Heidelberg University

summary: Single cells were isolated from the main scenarios during tumor dissemination of a highly metastatic Patient-Derived Xenograft model (Panc-265) in order to discover potential therapeutic targets against the metastatic settings of PDAC. Primary tumor (n=37), liver metastasis (n=23) cells and circulating tumor cells (CTCs, n=10, in bloodstream) were subjected of single-cell RNAseq. Single-cell RNA sequencing analysis revealed that CTCs clustered separately from their matched primary and metastatic tumors and were characterized by low expression of ECM associated genes, high expression of cell cycle genes, a metabolic switch to oxidative phosphorylation and high expression of genes involved in ribosome biogenesis.

overall_design: Cells enriched from primary tumor, mouse blood and liver of PDX metastatic model (Panc-265) were individually separated on the C1™ Single-Cell Auto Prep System (Fluidigm, South San Francisco, CA,USA) and cDNA amplification was generated  using the SMARTer®Ultra™ Low RNA kit for the Fluidigm C1™ System (Clontech, Mountain View, CA, USA). In total, 137 cells were captured on three C1 array chips for mRNA sequencing (17–25 μm Fluidigm). Cells that were negative for the human membrane marker and positive for a viability marker (DAPI) were excluded from further analysis. In total 70 samples passed the criteria. cDNA quantity and quality was measured with a 2100 Bioanalyzer (Agilent). Libraries were generated from 300 pg of amplified cDNA using the Nextera XT DNA Sample Prep Kit (Illumina) and sequenced on the HiSeq 2500 sequencer (Illumina) to generate 50 bases single reads at an average depth of 13.5 million reads per sample.

first: Manuel

last: Hidalgo

first: Fátima

last: Al-Shahrour

first: Pedro

middle: P

last: Lopez-Casas

first: Ana

last: Dopazo

last: Perales-Patón

first: Spas

last: Dimitrov Markov


title: In vivo isolated HER2/neu-Prim1 Primary, Residual, and Recurrent Tumor Cells, and Recurrent Tumor Stromal Cells

summary: Residual disease represents a major obstacle to the successful treatment of breast cancer, however little is known about the biology of residual tumor cells in vivo.  To identify genes differentially expressed in vivo in residual tumor cells compared to primary tumor cells or recurrent tumor cells, we used flow cytometry to isolate GFP-labeled tumor cells from primary, residual, or recurrent tumors grown orthotopically in nu/nu mice. WTA was used to amplify RNA from all tumor cells.

overall_design: Three timepoints (Primary tumor, residual disease, recurrent tumor) were taken with 3-4 replicates per timepoint.

first: Dhruv

last: Pant

first: Jason

last: Ruth


title: Single-cell epigenomics identifies a premetastatic regulatory program in lung adenocarcinoma [sciATAC-seq]

first: Lindsay

last: LaFave

overall_design: sciATAC-Sequencing profiles of normal lung and lung adenocarcinoma murine samples. We profiled 44 individual samples including 2 normal murine lungs, 1 CD45 depleted murine lungs, and 44 tdTom sorted KPT lung primary lung and metastatic samples. Species mixing experiments were also completed with GM12878 and 3T3 cell lines.


title: Ribosomal profiling of WT and mORF4/NBDY KO hearts

city: Utrecht

first: Eva

last: van Rooij

state: Utrecht

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: Left ventricles from the hearts of adult WT and mORR4/NBDY KO mice were obtained. Per heart, RNA-sequencing and ribosomal profiling was performed on the same heart

overall_design: Left ventricles of 4 hearts from wt mice and 5 heart from mORF4/NBDY KO mice were harvested. From each left ventricle the total RNA and ribosomal footprints were isolated.

first: Bas

last: Molenaar

first: Sebastiaan

last: van Kampen

first: Alexandre

last: Bossu

last: van Heesch

first: Jorge

last: Ruiz-Orera

first: Benedikt

last: Obermayer

first: Kamila

last: Kutz

first: Marta

last: Vigil-Garcia

first: Jantine

last: Monshouwer-Kloots

first: Mauro

last: Giacca

first: Norbert

last: Hubner

first: Toon

middle: B

last: van Veen

first: Teun

last: de Boer


title: The single-cellsequencing of purified wild type rat intervertebral disc (IVD) cells

city: shanghai

first: george

last: yue

address: Room 4B, the 3rd Building, No. 401, Caobao Road, Xuhui District, Shanghai, China, 200233

institute: Genergy Bio-technology (Shanghai) Co., Ltd

summary: IVDs are composed of heterogeneous cell groups, a further understanding of marker genes and cell phenotypes of healthy mature IVD cells is essential.

overall_design: The sample contained four wild-type 8-week-old male SD rats and four wild-type 8-week-old female SD rats.

first: Jingcheng

last: Wang

first: Yong

last: Huang


title: Transcriptome Assessment of Erythema Migrans Skin Lesions

city: Bethesda

first: Adriana

last: Marques

institute: NIAID/NIH

summary:
Gene arrays were used to characterize the global transcriptional alterations in skin biopsy samples of EM lesions in comparison to controls. The transcriptional pattern in EM biopsies consisted of 254 differentially regulated genes (180 induced and 74 repressed) characterized by the induction of chemokines, cytokines, Toll-like receptors, antimicrobial peptides, monocytoid cell activation markers, and numerous genes annotated as interferon (IFN)-inducible. The IFN-inducible genes included 3 transcripts involved in tryptophan catabolism (IDO1, KMO, KYNU) that play a pivotal role in immune evasion by certain other microbial pathogens by driving the differentiation of regulatory T cells.
PMCID: PMC5853807

overall_design: We utilized whole-genome arrays to characterize the global transcriptional alterations in skin biopsy samples of adult patients with erythema migrans (EM) in comparison to skin from healthy controls. Skin samples were collected by punch biopsy from the periphery of the primary  erythema migrans (EM) lesion of 18 subjects, and from 11 healthy volunteers (HV). Surgical control (SC) skin samples were obtained from specimens of 16 anonymous donors undergoing surgery for other purposes.


title: Bulk-ATAC sequencing in RUNX-altered murine lung adenocarcinoma cell lines

first: Lindsay

last: LaFave

summary: Here, we using CRISPR activation and knockout studies to assess the implication of dysregulation of RUNX transcription factors on chromatin accessibility using bulk ATAC-sequencing. Tumor cell lines were derived from primary Kras G12D; p53 mutant mice (KP model) after initiation of tumors with SPC-Cre, resulting in lung adenocarcinoma. Cell lines were then expanded and profiled using bulk ATAC-sequencing.

overall_design: Primary tumor derived cell lines were modified using CRISPR knockout and activation. Bulk ATAC-sequencing was completed on these cell lines.

first: Vinay

last: Kartha


title: Changes in Growth Performance, Physiological Parameters, and Lipid Metabolism-related Genes Expression of Hybrid Yellow Catfish (Tachysurus fulvidraco ♀ × Pseudobagrus vachellii ♂) following different dietary Acanthopanax Senticosus levels

city: 无锡

first: 李

middle: 鸣

last: 霄

address: 滨湖区雪浪街道南泉薛家里69号无锡渔业学院

institute: 中国水产科学研究院淡水渔业研究中心

summary: High-density aquaculture and over-nutrition may cause fatty liver disease in hybrid yellow catfish, reduce the quality of fish products, and limit the development of the industry. In this experiment, Acanthopanax senticosus powder was used as an additive for hybrid yellow catfish feed. A control group (fed on a diet without A.senticosus) and five groups fed on diets supplemented with A.senticosus (0.5, 1, 2, 4 and 8 g A.senticosus / kg). To study the effects of A.senticosus on the growth performance and physiological parameters of hybrid yellow catfish, and to determine the effect of A.senticosus on the expression of genes related to lipid metabolism in the liver by transcriptome analysis. It was found that dietary supplementation with A.senticosus at 2-4g/kg can promote the growth of yellow catfish, reduce the levels of total cholesterol and triacylglycerol in serum, and increase the activity of fatty acid synthase involved in lipid transport in the liver. Gene expression profiles in the liver were compared between the control group and 4g/kg A.senticosus group, and 5 differentially expressed genes in these groups were identified. Annotation analyses using tools at the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases showed that these five differentially expressed genes were mainly involved in the regulation of fat metabolism. The experimental results show that adding a suitable amount of A.senticosus in the diet can reduce the expression of FADS2, ELOVL2, and PLPP3 genes in the liver and stimulate the expression of CYP24a gene, which will reduce the contents of TG and TC in the body, reduce the deposition of fat in the tissue, and promote lipid Metabolism to achieve the purpose of protecting the liver. Therefore, A.senticosus can be used as a healthy feed additive for hybrid yellow catfish, and the appropriate content in the diet is 2-4g/kg.

sample_organism: Tachysurus fulvidraco x Tachysurus vachelli

overall_design: Transcriptome analysis of hybrid yellow catfish fed with 4g/kg Acanthopanax senticosus and yellow catfish fed with 0g/kg Acanthopanax basal feed for 56 days

first: Li

last: Xiao

first: Qiang

last: Jun

first: Xu

last: Pao

first: Bao

middle: J

last: Wen

first: Tao

middle: Y

last: Fan

first: Zhu


title: Investigating the role of DOCK8 in T follicular helper cells positioning and function in germinal centers

city: Boston

first: Erin

last: Janssen

state: Massachusetts

address: 1 Blackfan St, Karp 10

institute: Boston Children's Hospital/Harvard Medical School

summary: T follicular helper (Tfh) cell migration into germinal centers (GC) is essential for the generation of GC B cells and antibody responses to T dependent (TD) antigens. This process requires interactions between LFA-1 on Tfh cells and ICAMs on B cells. The mechanisms underlying defective antibody responses to TD antigens in DOCK8 deficiency are incompletely understood. We show that mice selectively lacking DOCK8 in T cells have impaired IgG antibody responses to TD antigens, decreased GC size, and reduced numbers  of GC B cells. However, they develop normal numbers of Tfh cells with intact capacity for driving B cell differentiation into a GC phenotype in vitro. Notably, migration of DOCK8 deficient T cells into GCs is defective. Following TCR/CD3 ligation, DOCK8 deficient T cells have impaired LFA-1 activation and reduced binding to ICAM-1. DOCK8 is important for LFA1-dependent positioning of Tfh cells in GCs, and thereby the generation of GC B cells and IgG antibody responses to TD antigen.

overall_design: RNA seq analysis of mouse T follicular helper (Tfh)  (CD4+CD19-CD25-CXCR5+ICOS+) sorted from popliteal and inguinal Lymph nodes of Cd4-CreTgDock8flox/flox and control mice immunized in the hock with TNP-KLH

first: Mira

last: Tohme

first: Raif

last: Geha


title: The minor spliceosome is required for limb growth but not patterning

status: Public on Jul 22 2020

city: Storrs

first: Rahul

middle: N

last: Kanadia

state: CT

address: 75 N. Eagleville Road

department: Physiology and Neurobiology

institute: University of Connecticut

summary: Diseases caused by mutations in components of the minor spliceosome frequently result in primordial dwarfism, where the limbs are stunted in size but retain pattern. We therefore sought to determine the role of the minor splieceosome in limb development by ablating an essential component, Rnu11, which encodes the U11 snRNA, in the mouse limb bud through Prrx1-Cre. We found that loss of U11 results in severe reduction in limb size at birth. However, mutant limbs retain proximo-distal patterning. Thus, we performed total RNAseq at E10.5 and E11.5 for both WT and mutant forelimb and hindlimb to determine the underlying molecular consequence of U11 loss and its effect on gene expression in the developing limb.

overall_design: Total mRNA profiles of forelimb (FL) and hindlimb (HL) buds dissected from E10.5 and E11.5 n=3 WT and mutant mice through TruSeq stranded total RNA prep followed by Illumina NextSeq500 with high output.

first: Kyle

last: Drake


title: Seminal plasma modulates miRNA expression by sow genital tract lining explants

city: Girona

first: Isabel

last: Barranco

state: CATALUñA

address: Calle Maria Aurèlia Campany, 69, Facultad de Ciencias

country: Spain

institute: University of Girona

summary:
The seminal plasma (SP) modulates the female reproductive immune environment after mating and microRNAs (miRNAs) could participate in the process. Considering the boar ejaculate is built by fractions differing in SP-composition; this study evaluated whether exposure of mucosal explants of the sow internal genital tract (uterus, utero-tubal junction and isthmus) to different SP-fractions changed the profile of explant-secreted miRNAs. Mucosal explants retrieved from oestrus sows (n=3) were in vitro exposed to: Medium 199 (M199, Control) or M199 supplemented (1:40 v/v) with SP from the sperm-rich fraction (SRF), the post-SRF or the entire recomposed ejaculate, for 16 h. After, the explants were cultured in M199 for 24 h to finally collect the media for miRNA analyses using GeneChip miRNA 4.0 Array (Affymetrix).
Fifteen differentially expressed (False‐Discovery-Rate < 0.05 and Fold-change ≥ 2) miRNAs (11 down- vs 4 up-regulated) were identified (the most in the media of uterine explants incubated with SP from post-SRF). Bioinformatics analysis identified that predicted target genes of dysregulated miRNAs, mainly miR-34b, miR-205, miR-4776-3p and miR-574-5p, were involved in functions and pathways related to immune response. In conclusion, SP is able to elicit changes in the miRNAs profile secreted by female genital tract, ultimately depending SP-composition.

overall_design: In vitro exposure of mucosal explants of the internal genital tract of three oestrus sows (uterus, utero-tubal junction [UTJ] and isthmus) to Medium 199 (M199) alone or M199 supplemented with SP from different fractions (i.e. the sperm-rich fraction [SRF], the post-SRF) or a composite (recomposed entire ejaculate [EE]) for 16 h. After, the explants were cultured in M199 for 24 h to finally collect the media for miRNA analyses using GeneChip miRNA 4.0 Array (Affymetrix).

first: Lorena

last: Padilla

first: Cristina

middle: A

last: Martinez

first: Manuel

last: Alvarez-Rodriguez

first: Inmaculada

last: Parrilla

first: Xiomara

last: Lucas

first: Graça

last: Ferreira-Dias

first: Marc

last: Yeste

first: Heriberto

last: Rodriguez-Martinez

first: Jordi

last: Roca


title: Microarray Profile of Long Noncoding RNA and Messenger RNA Expression in a Model of Alzheimer’s Disease

city: Beijing

first: li

last: zeng

state: Beijing

address: Institute of Medical Biotechnology, Tiantan Xili, Dongcheng District, Beijing

institute: Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: our study aimed to understanding the pathological hallmarks and looking for effective therapeutic targets based on the altered lncRNA level of AD, which may be suggested to act as “markers” to distinguish the pathological changes of this disease.

overall_design: In our study, we chose 1-month-old, 3-month-old, 6-month-old, and 9-month-old APP/PS1 mice and their respective age-matched WT control mice to accomplish our analysis. Each age group contains three male mice as well as their WT controls.

first: Rui

last: Liu

first: Zhuorong

last: Li

first: Linlin

last: Wang

first: Li

last: Zeng

first: Hailun

last: Jiang


title: Single-cell epigenomics identifies a premetastatic regulatory program in lung adenocarcinoma

first: Lindsay

last: LaFave


title: Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer’s Disease

city: Leuven

first: Bart

last: De Strooper

address: O&N4 Herestraat 49

department: Centre for Brain and Disease research

country: Belgium

institute: VIB - KU Leuven

summary: While complex inflammatory-like alterations are observed around the amyloid plaques of Alzheimer disease (AD), little is known about the molecular changes and cellular interactions that characterize this response. We investigate here in an AD mouse model the transcriptional changes occurring in tissue domains of 100 μm diameter around the amyloid plaques using spatial transcriptomics. We demonstrate early alterations in a gene co-expression network enriched for myelin and oligodendrocyte genes (OLIG), while a multicellular gene co- expression network of Plaque-Induced Genes (PIGs) involving the complement system, oxidative stress, lysosomes and inflammation is prominent in the later phase of the disease. We confirm the majority of the observed alterations at the cellular level using in situ sequencing on mouse and human brain sections. Genome-wide spatial transcriptomic analysis provides an unprecedented approach to untangle the dysregulated cellular network in the vicinity of pathogenic hallmarks of AD and other brain diseases.

overall_design: In situ 2D-RNAseq via Spatial Transcriptomics  on coronal section of AppNL-G-F KI mice and C57Bl/6J  mice at 3,6,12 and 18 months of age.

first: Wei-Ting

last: Chen

first: Ashley

last: Lu

first: Katleen

last: Craessaerts

first: Benjamin

last: Pavie

first: Carlo

middle: S

last: Frigerio

first: Nikky

last: Corthout

first: Xiaoyan

last: Qian

first: Jana

last: Lalakova

first: Malte

last: Kühnemund

first: Iryna

last: Voytyuk

first: Leen

last: Wolfs

first: An

last: Snellinx

first: Sebastian

last: Munck

first: Aleksandra

last: Jurek

first: Jose

middle: F

last: Navarro

first: Takaomi

middle: C

last: Saido

first: Joakim

last: Lundeberg

first: Mark

last: Fiers


title: OGT suppresses macrophage proinflammatory activation

city: New Haven

first: Xiaoyong

last: Yang

address: 375 Congress Ave

department: Comparative Medicine

institute: Yale University

summary: Overnutrition leads to metabolic disorders such as obesity and diabetes. Enhanced inflammation has also been shown to be an essential player in the progression of metabolic diseases. However, how immune cells sense nutritional status and contribute to whole-body metabolism remain largely elusive. OGT-catalyzed protein O-GlcNAcylation is thought to be a metabolic sensor that modulates cell signaling. In this study, we show that overnutrition stimulates macrophage O-GlcNAc signaling. O-GlcNAc signaling suppresses macrophage proinflammatory activation and protects against diet-induced obesity and metabolic dysfunction. These findings thus identify macrophage O-GlcNAc signaling as a novel homeostatic regulator at the interface of inflammation and metabolism.

overall_design: Unstimulated (M0), LPS (100 ng/ml, 12 hours)-stimulated (M1) and IL-4 (10 ng/ml, 12 hours)-stimulated (M2) WT and OGT knockout (KO) mouse bone marrow-derived macrophages (BMDMs) were collected. Then total RNA was extracted and used for RNA sequencing-based transcriptional profiling.

first: Yunfan

first: Jin

last: Nam

first: Dongjun

last: Chung


title: Development of circRNA expression signatures in Tregs from psoriatic patients and healthy controls

city: Xi'an

first: luting

state: Shaanxi

address: No.620, South Chang’an Road, Xi’an, 710062, China

institute: Shaanxi normal university

summary:
In order to analyze and find differentially expressed circRNAs in Treg from psoriatic and healthy controls, we aimed to explore whether differentially expressed circRNAs in psoriatic patients could account for the dysfunctional Tregs in psoriasis patients
could account for dysfunctional Tregs in psoriatic patients

overall_design: Tregs are isolated by flow cytometry from PBMCs of 3 healthy controls and psoriatic patients

first: Luting

first: Chen

last: Zhang

first: Gang

last: Wang


title: Next Generation Sequencing Facilitates Quantitative Analysis of the effects of DR-3 agonist on sorted mouse VAT ILC2 Transcriptomes

city: Los Angeles

first: Pedram

last: Shafiei Jahani

state: CA

address: 1450 Biggy Street NRT 5509

department: MMI

institute: USC

summary: Disturbances in glucose homeostasis and low-grade chronic inflammation culminate into metabolic syndrome that increase the risk for the development of type 2 diabetes mellitus (T2DM). The recently discovered type 2 innate lymphoid cells (ILC2s) are capable of secreting copious amounts of type 2 cytokines to modulate metabolic homeostasis in adipose tissue. In this study, we have established that expression of Death Receptor 3 (DR3), a member of the TNF superfamily, on visceral adipose tissue (VAT)-derived murine and peripheral blood human ILC2s is inducible by IL-33. We demonstrate that DR3 engages the canonical and/or non-canonical NF-B pathways, and thus stimulates naïve and co-stimulates IL-33-activated ILC2s. Importantly, DR3 engagement on ILC2s significantly ameliorates glucose tolerance, protects against insulin-resistance onset and remarkably reverses already established insulin-resistance. Taken together, these results convey the potent role of DR3 as an ILC2 regulator and introduce DR3 agonistic treatment as a novel therapeutic avenue for treating T2DM.

overall_design: mRNA profiles of sorted mouse VAT ILC2s from WT (treated with DR3 agonist or iso control) mice were generated by deep sequencing, in triplicate or duplicate, using a NextSeq 500 (Illumina) system.

first: P

first: O

last: Akbari


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and non-antibiotic pharmaceuticals stressed Acinetobacter baylyi ADP1 Transcriptomes

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

country: Australia

institute: University of Queensland

summary: The goals of this study are to use Next-generation sequencing (NGS) to detect bacterial mRNA profiles of wild-type A.baylyi ADP1, and its mRNA response under the exposure of six non-antibiotic pharmaceuticals, including ibuprofen, naproxen, gemfibrozil, diclofenac, propanolol, and iopromide. The concentrations were 0.5 mg/L for ibuprofen, naproxen, gemfibrozil, diclofenac, propanolol, and 1.0 mg/L for iopromide. The group without dosing pharmaceutical was the control group. Each concentration was conducted in triplicate. By comparing the mRNA profiles of experimental groups and control group, the effects of these six non-antibiotic pharmaceuticals on transcriptional levels can be revealed. Illumina HiSeq 2500 was applied. The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp. The clean reads of each sample were aligned to the A.baylyi ADP1 reference genome (NC_005966.1), using SeqAlto (version 0.5). Cufflinks (version 2.2.1) to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R. (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.

overall_design: Bacterial mRNA profiles of wild-type A.baylyi ADP1, in response to 0.5 mg/L ibuprofen, 0.5 mg/L naproxen, 0.5 mg/L gemfibrozil, 0.5 mg/L diclofenac, 0.5 mg/L propanolol, and 1.0 mg/L  iopromide for 2 hours, bacteria without dosing pharmaceutical are the control group, in triplicate, using Illumina HiSeq 2500

first: Yue

first: Likai

last: Mao


title: Regulatory T cells license macrophage pro-resolving functions in atherosclerosis regression

city: New York

first: Emily

last: Brown

state: NY

address: 435 E 30th St

department: Medicine

institute: NYU Langone

summary: Regression of atherosclerosis is an important clinical goal, however the pathways that mediate the resolution of atherosclerotic inflammation and reversal of plaques are poorly understood. Regulatory T cells (Tregs) have been shown to be atheroprotective, however numbers of these immunosuppressive cells decrease with disease progression. Using multiple independent mouse models of atherosclerosis regression, we demonstrate that an increase in plaque Tregs is a common signature of regressing plaques. To test if Tregs are required for the resolution of atherosclerotic inflammation and plaque regression during lipid-lowering therapy, we combined CD25 monoclonal antibody (PC61 mAb)-mediated Treg depletion with single-cell RNA-sequencing of immune cells in the plaque and conventional analyses of atherosclerosis. Single cell RNA-sequencing revealed that Tregs from aortic plaques shared some similarity with splenic Tregs, but were distinct from skin and colon Tregs supporting recent findings of tissue-dependent Treg heterogeneity. Furthermore, Tregs from progressing plaques expressed markers of natural Tregs derived from the thymus, whereas Tregs in regressing plaques lacked Nrp1 and Helios expression, suggesting that they are induced in the periphery during lipid lowering. Treatment of atherosclerotic mice with PC61 mAb effectively depleted Tregs in the blood and peripheral tissues, including plaques, and blocked the regression of atherosclerosis induced by apoB anti-sense oligonucleotides. Morphometric analyses revealed that control antibody-treated mice showed a 40% decrease in plaque burden and macrophage content under regression conditions, whereas PC61 mAb-treated mice showed no change in plaque size or inflammatory cell content compared to baseline. Moreover, Treg depletion enhanced inflammatory signaling and blocked tissue reparative functions of macrophages in the regressing plaque, including M2-polarization, efferocytosis and sensing of specialized pro-resolving lipid mediators. Together, these data establish essential roles for Tregs in the resolution of atherosclerotic inflammation and plaque remodeling during regression.

overall_design: Single cell RNA sequencing of aortic sorted CD45+ cells from atherosclerotic C57BL/J6 mice (n=12, 1012 AAV-PCSK9 at 8wk old mice, then WD for 20 wks). Then 4 mice on WD were used as progression group, 2979 cells identified, Using Illumina HiSeq4000.  The other 8mice were switched into chow diet for further 3 wks and also i.p. treated with ApoB-ASO (50 mg/kg, total of 2 doses in first week) as regression groups. 4 mice were either treated with IgG control antibody and 4 mice were treated with anti-CD25 antibody. 1782 cells from control and 2357 cells from treated groups were identified, using Illumina HiSeq4000.

first: Monika

last: Sharma

middle: M

last: Schlegel

first: Milessa

last: Afonso

first: Karishma

last: Rahman

first: Ada

last: Weinstock

first: Brian

middle: E

last: Sansbury

first: Emma

last: Corr

first: Coen

last: van Solingen

first: Graeme

last: Koelwyn

first: Lianne

last: Shanley

first: Lauren

last: Beckett

first: Daniel

last: Peled

first: Juan

last: Lafaille

first: Matthew

last: Spite

first: P'ng

last: Loke

first: Edward

last: Fisher

first: Kathryn

last: Moore


title: Expression data from isolated areas from [Apc-Arid1a]ko-focal liver tissues after FFPE treatment

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

summary: We used microarrays to analyse differences between red blood cell region, adjacent region or healthy tissue,

overall_design: After sacrifice of mice presenting peliosis-like areas or control ones, livers were harvested, fixed overnight in 4% formalin buffer, and embedded in paraffin. Healthy (N=4), adjacent (N=4) and peliosis-like areas (N=4) were isolated from 15 to 20 paraffin sections. After deparaffinization, FFPE tissues were lysed for 24h in tissue lysis buffer supplemented with proteinase K at 60C. and total RNA were extracted from tissue sections with Trizol reagent. After  purification, RNA was quantified. Then, RNA was analyzed with microarrays.

first: Sabine

last: Colnot

first: Rozenn

last: Riou


title: KLF3 mediates epidermal differentiation through the epigenomic writer CBP

city: La Jolla

first: George

last: Sen

state: California

address: 9452 Medical Center Dr.

department: Dermatology

institute: University of California San Diego

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

overall_design: Refer to individual Series

first: Jackson

last: Jones


title: KLF3 mediates epidermal differentiation through the epigenomic writer CBP [ChIP-seq]

summary: The differentiated layers of the epidermis protect the body from the outside environment. Impairments in the differentiation process can lead to skin diseases that can afflict ~20% of the population. Thus, it is of utmost importance to characterize and understand the factors that promote the differentiation process. Here we identify the transcription factor KLF3 as a novel regulator of epidermal differentiation. Knockdown of KLF3 results in reduced differentiation gene expression and increased cell cycle gene expression. Over 50% of KLF3’s genomic binding sites occur at regions containing H3K4me/H3K27ac with the vast majority at active enhancers. KLF3 bound to active enhancers proximal to differentiation genes that are dependent upon KLF3 for expression. Based on this association, we sought to investigate KLF3’s possible relationship with the enhancer associated proteins CBP and P300. Analysis of the transcriptome controlled by CBP and P300 showed that CBP and KLF3 control a similar gene expression program and are both essential for promoting differentiation.  In addition, 35% of CBP’s genomic binding sites overlap with KLF3 and knockdown of KLF3 results in reduced CBP localization at enhancers proximal to differentiation gene clusters. Our results suggest that KLF3 regulates differentiation gene expression by promoting CBP localization at enhancers.

overall_design: KLF3 and CBP ChIP seq in day 3 differentated primary keratinocytes. KLF3 knockdown ChIP-seq using CBP antibody


title: Expression data from DE-71 treated rats at PND4

city: RTP

first: Keith

last: Shockley

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

summary:
To identify liver transcripts differentially expressed between control samples and animals exposed to DE-71, we collected RNA from male pups at postnatal day 4 (PND4) after the Wistar Han dams were exposed to 0, 0.1, 15, or 50 mg/kg DE-71.  These samples were interrogated with the Affymetrix Rat Genome 230 2.0 GeneChip array
A total of 0, 15, and 162 gene transcripts were differentially expressed between control samples and 0.1, 15, and 50 mg/kg DE-71, respectively (using a false discovery rate (FDR) threshold of 0.05). These transcripts were mapped to 0, 13, and 161 genes using Ingenuity Pathway Analysis.

overall_design: There were 4 groups and 5x replication for each group, except there were only 4 samples for the 15 mg/kg group, for 19 total samples. The groups were (1) vehicle control, (2) 0.1 mg/kg DE-71, (3) 15 mg/kg DE-71, and (4) 50 mg/kg DE-71. We compared vehicle control vs the dose group using the R/maanova package. The differentially expressed transcripts were identified based on a false discovery rate threshold of 0.05.

middle: R

first: June

middle: K

last: Dunnick


title: Global transcriptional profiling of tyramine and D-glucuronic acid catabolism in Salmonella

city: Pullman

first: Raquel

middle: Cristina

last: Konrad Burin

state: WA

address: 155N Bustad Hall

department: Veterinary Microbiology and Pathology

institute: Washington State University

summary: Previously we reported that Salmonella can proliferate by deriving energy from two metabolites that naturally occur in the host as gut microbial metabolic byproducts, namely, tyramine (TYR, an aromatic amine) and D-glucuronic acid (DGA, a hexuronic acid). Salmonella Pathogenicity Island 13 (SPI-13) plays a critical role in the ability of Salmonella to derive energy from TYR and DGA, however the catabolism of these two micronutrients in Salmonella are poorly defined. The objective of this study was to identify the specific genetic components and the regulatory circuits for the construction of the TYR and DGA catabolic pathways in Salmonella. To accomplish this, we employed TYR and DGA-induced global transcriptional profiling and gene functional network analysis.

sample_organism: Salmonella enterica subsp. enterica serovar Enteritidis

overall_design: The experimental matrix included 3 conditions x 3 biological replicates/condition, resulting in a total of 9 independent samples

last: Burin

first: Devendra

last: Shah


title: Expression data from PBDE-47 and DE-71 treated rats at PND4


title: The cytokine IL-17A limits Th17 pathogenicity via a negative feedback loop driven by autocrine induction of IL-24

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: Dysregulated Th17 cell responses underlie multiple inflammatory and autoimmune diseases, including autoimmune uveitis and its animal model, EAU. However, clinical trials targeting IL-17A in uveitis were not successful. Here, we found that Th17 cells were regulated by their own signature cytokine, IL-17A. Loss of IL-17A in autopathogenic Th17 cells did not reduce their pathogenicity and instead elevated their expression of the Th17 cell cytokines GM-CSF and IL-17F. Mechanistic in vitro studies revealed a Th17 cell-intrinsic autocrine loop triggered by binding of IL-17A to its receptor, leading to activation of transcription factor NFκB and induction of IL 24, which repressed the Th17 cytokine program. In vivo, IL-24 treatment ameliorated Th17-induced EAU, whereas silencing of IL-24 in Th17 cells enhanced disease. This regulatory pathway also operated in human Th17 cells. Thus, IL-17A limits pathogenicity of Th17 cells by inducing IL-24. These findings may explain the disappointing therapeutic effect in targeting IL-17A in uveitis.

overall_design: Three biological replicates were analyzed for each of 2 conditions (two genotypes - Wildtype WT and IL-17A Knockout KO)

first: Rachel

last: Caspi

first: Wai

last: Chong

first: Mary

last: Mattapallil


title: Expression data from PBDE-47 treated rats at PND4

summary:
To identify liver transcripts differentially expressed between control samples and animals exposed to PBDE-47, we collected RNA from male pups at postnatal day 4 (PND4) after the Wistar Han dams were exposed to 0, 0.1, 15, or 50 mg/kg PBDE-47.  These samples were interrogated with the Affymetrix Rat Genome 230 2.0 GeneChip array.
A total of 7, 50, and 149 gene transcripts were differentially expressed between control samples and 0.1, 15, and 50 mg/kg PBDE-47 (using a false discovery rate (FDR) threshold of 0.05). These transcripts were mapped to 2, 40, and 139 genes using Ingenuity Pathway Analysis.

overall_design: There were 4 groups and 5x replication for each group, for 20 total samples. The groups were (1) vehicle control, (2) 0.1 mg/kg PBDE-47, (3) 15 mg/kg PBDE-47, and (4) 50 mg/kg PBDE-47. We compared vehicle control vs the dose group using the R/maanova package. The differentially expressed transcripts were identified based on a false discovery rate threshold of 0.05.


title: Structural and biochemical analyses of Caulobacter crescentus ParB reveal the role of its N-terminal domain in chromosome segregation

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

institute: John Innes Centre

summary: The tripartite ParA-ParB-parS complex ensures faithful chromosome segregation in the majority of bacterial species. ParB nucleates on the centromere-like parS site and spreads to neighboring DNA to form a network of protein-DNA complexes. This nucleoprotein network in turn interacts with ParA to partition the parS locus, hence the chromosome to each daughter cell. Here, we determine the co-crystal structure of the C-terminal domain truncated ParB-parS complex from Caulobacter crescentus, and show that its N-terminal domain is inherently flexible and adopts multiple different conformations. We propose that the flexibility of the N-terminal domain might facilitate the spreading of ParB on the chromosome. Next, using ChIP-seq we show that ParBs from different bacterial species exhibit variation in their intrinsic capability for spreading, and that the N-terminal domain rather than the C-terminal domain is the main determinant for the variation in spreading. Finally, we show that the C-terminal domain of Caulobacter ParB does not possess non-specific DNA-binding activity in vitro. Engineered ParB variants with enhanced non-specific DNA-binding activity condense DNA in vitro but do not spread further than a wild-type protein in vivo. Taken together, our results emphasize the central role of the N-terminal domain in ParB spreading and faithful chromosome segregation.

sample_organism:
Escherichia coli
Caulobacter vibrioides NA1000

overall_design: Chromatin-immunoprecipitation with deep sequencing experiments (ChIP-seq) were performed on exponential-growing Escherichia coli and Caulobacter crescentus.

first: T

first: N

middle: T

last: Tran

first: A

last: Jalal

first: S

last: Stevenson

first: D

last: Lawson

first: F

last: Moreno-Herrero

first: C

middle: L

last: Pastrana


title: Acute hypoxia changes the utilization mode of glucose / lipid in the liver of the largemouth bass (Micropterus salmoides)

city: Haikou

first: JunLong

last: Sun

state: Hainan

address: No.58 Renmin Avenue, Haikou City, Hainan Province

institute: Hainan University

summary: In the present study, we used NGST to characterize mRNA-seq of control-, moderate hypoxia-treated and severe hypoxia-treated Micropterus salmoides livers to elucidate the molecular mechanisms of hypoxia adaptation. This is the first report on integrated analysis of the tissue specific and temporal changes in gene expression in largemouth bass (Micropterus salmoides) exposed to hypoxia could reveal mechanisms of hypoxia adaptation. We provide a good case study with which to analyse mRNA expression and profile non-model fish species using NGST.

overall_design: We used RNA sequencing to detect mRNA transcriptomes of liver from largemouth bass with moderate hypoxia group (MHG) and severe hypoxia group (SHG) compared them with control group (CG) under 0h, 4h, 8h, 12h, and 24h (3 vs. 3).

first: Junlong

first: Song

last: Yang


title: Transcriptional profiling of Saccharomyces cerevisiae WT and set4∆ strains during hypoxia

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

summary: Purpose: The goal of this study was to globally characterize the transcript levels of genes in Saccharomyces cerevisiae WT and set4∆ strains during hypoxia. Using transcriptome profiling of isogenic WT and set4∆ strains grown under aerobic or 8 hours of hypoxia. We analyzed the changes in gene expression that occur during aerobic and hypoxic conditions and identified sets of upregulated and downregulated gene expression.

overall_design: Method: Total RNA extracted from WT and set4∆ cells grown under aerobic or 8 hours of hypoxia was used to generate cDNA libraries using the TruSeq Stranded Kit with PolyA selection (Illumina) system. Nine RNA samples were barcoded, pooled and sequenced using the Illumina HiSeq2500 next generation sequencer using the rapid run mode (three biological replicates for each strain and conditiong including the WT aerobic condition, WT hypoxic condition and set4∆ hypoxic condition).

first: Nina

last: Serratore

first: Vikki

last: Weake

first: Scott

middle: D

last: Briggs


title: β-catenin inhibits adipogenic differentiation of hypertrophic chondrocytes and promote osteogenesis

city: Pok Fu Lam

first: Peikai

last: Chen

address: Sassoon Road 5

country: Hong Kong

institute: The University of Hong Kong

summary: It has been shown that hypertrophic chondrocyte (HC) can become osteoblast, contributing to the formation of trabecular bone and endosteum. However, it is unclear what genes regulate the process of differentiation from chondrocyte to osteoblast. Conditional knock-out of β‑catenin in HCs can reduce the trabecular bone amount and there is also some evidence that ablation of β‑catenin in HCs can promote bone marrow adipogenesis. Conditional stabilization of β‑catenin in HCs results in osteopetrosis. In order to investigate the gene regulatory network with different dosage of β‑catenin in HC descendants (i.e. in Loss-of-Function mutant, Gain-of-Function mutant and Wildtype control), we collected HC descendant cells from proximal tibia of mice at postnatal day 5 and performed bulk RNA seq to profile the gene expression pattern in HC descendants.

overall_design: We sequenced 8 bulk RNAseq samples. Cells were harvested from proximal tibia and only the hypertrophic chondrocyte descendants were collected for RNAseq. Four of them are on Col10a1Cre;Rosa26-Tdtomato;Ctnnb1Δ/Δ (b-cat LoF mutant), two of them are Col10a1Cre;Rosa26-Tdtomato;Ctnnb1-exon3 Δ/+ (b-cat GoF mutant), and the remaining two are Col10a1Cre;Rosa26-Tdtomato (wildtype control). 70 tdTomato-expressing cells were manually picked under fluorescent microscope, pooled and subject to Smart-seq2 protocol.

first: Kwok

last: Tsang

first: Kathy

last: Cheah


title: Gene expression profiles in maspin-overexpressing MDA-MB-231 breast cancer cells

city: Yonago

first: Tomohiko

last: Sakabe

state: Tottori

address: Nishi-cho 86

country: Japan

institute: Tottori University

summary: A comparison of gene expression profiles between control- and mascpin-overexpressing MDA-MB-231 cells was performed to investigate the role of cytoplasmic maspin in breast cancer progression. The data provides insight into the importance of cytoplasmic maspin in  breast cancer progression.

overall_design: MB-231-control and MB-231-maspin cells were established by stable transduction with lentivirus-based vector. Total RNA from these cells were recovered using Rneasy Mini Kit. Isolated RNA was labeled by Cy5 and hybridized onto the 3D-Gene human mRNA oligo chip 25k (Ver 2.1). Oligo chip was scanned by a 3D-Gene Scanner 3000.

first: Yoshihisa

last: Umekita


title: Single cell RNA-seq of mouse cardiac cells: postnatal 3 weeks

status: Public on Jul 21 2020

city: Shanghai

first: Zhen

last: Jiang

state: Shanghai

address: 393 Middle Huaxia Road, L Building B328

department: Life Science and Technology School

institute: ShanghaiTech University

summary: We performed lineage tracing studies using various genetic models, and found that cardiac mesenchymal cells (MCs) contribute to CAs in postnatal development and adult homeostasis. We found that PDGFRb+ cells are heterogenous, and demonstrated that PDGFRb+ MCs, but not NG2+ coronary vascular mural cells, are the major source of intramyocardial adipocytes. We performed single cell RNA sequencing to compare the heterogeneity.

overall_design: Single cardiac cells were isolated from infant mouse at postnatal 3 weeks by retrograde Langendorff  perfusion, Single cell library was generated using 10x Genomic Chromium system with the v3 single cell  reagent kit. Sequencing of library was performed on Illumina NovoSeq 6000 platform.

first: Hui

last: Zhang


title: The osteocyte transcriptome is extensively dysregulated in mouse models of Osteogenesis Imperfecta

city: Little Rock

first: Roy

last: Morello

state: AR

address: 4301 W. Markham St #505

department: Physiology and Biophysics

institute: University of Arkansas for Medical Sciences

summary: Osteocytes are long-lived, highly interconnected, terminally differentiated osteoblasts which reside within mineralized bone matrix. They constitute about 95% of adult bone cells and play important functions in the regulation of bone remodeling, phosphate homeostasis, and mechanical stimuli sensing and response. However, the role of osteocytes in the pathogenesis of congenital diseases of bone such as osteogenesis imperfecta (OI) is poorly understood. This study characterized in vivo transcriptional changes in osteocytes from the CrtapKO and oim/oim mouse models of OI, using RNA-sequencing on osteocyte-enriched cortical bone from femur and tibia. These models were chosen because they mimic two types of OI with different genetic mutations which result in distinct type I collagen defects. Hundreds of transcripts were dysregulated in either model of OI compared to WT, but 281 of these were similarly up- or down-regulated in both. Conversely, very few transcripts were differentially expressed between the CrtapKO and oim/oim mice, indicating that distinct alterations in type I collagen can lead to shared pathogenic processes and similar phenotypic outcomes. Bioinformatics analyses identified several critical hubs of dysregulation that were enriched in annotation terms such as development and differentiation, ECM and collagen fibril organization, cell adhesion, signaling, regulatory processes, pattern binding, chemotaxis, and cell projections. The data further indicated alterations in important signaling pathways such as WNT and TGF-β. Overall, our study suggested that the osteocyte transcriptome is broadly dysregulated in OI, that transcriptomic alterations in OI can be strikingly similar despite arising from different genetic mutations, and that the potential consequences of osteocyte dysregulation deserve further investigation.

overall_design: RNA sequencing was performed on mRNA isolated from osteocyte-enriched cortical bone (OT-rich bone) of 3-month old WT, CrtapKO, and oim/oim mice (4 biological replicates of each genotype).

first: Sarah

last: Zimmerman

first: Milena

last: Dimori

first: Melissa

last: Heard-Lipsmeyer


title: PC-3M-1E8 transcriptome

city: Peking

first: wang

middle: li

last: yong

state: Peking

address: No 10 xi tou tiao, you an gate

department: medical school

institute: Capital Medical University

summary: The transcriptome sequencing analyse the differential expression genes between scramble and nc886+ cells

overall_design: RNA seq of PC-3M-1E8

first: L

last: Kong

last: Wang


title: Transcriptome datasets of the Quaking (QKI) gene knock-down human oral squamous cell carcinoma (OSCC) cells

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

institute: Dankook University

summary: Here, we elucidated whether miR-200 family members control RNA-binding protein quaking (QKI), a newly identified tumor suppressor that is regulated during EMT. QKI expression was suppressed by miR-200 overexpression, and the 3'-UTR of QKI mRNA was directly targeted by miR-200 in luciferase reporter assays. ShRNA-mediated knockdown of QKI led to pronounced EMT and protumor effects in both in vitro and in vivo studies of oral squamous cell carcinoma. Furthermore, high expression of QKI protein is associated with favorable prognosis in surgically resected head and neck squamous cell carcinoma and lung adenocarcinoma. In conclusion, QKI increases during EMT and is targeted by miR-200; while, it suppresses EMT and tumorigenesis. We suggest that QKI and miR-200 form a negative feedback loop to maintain homeostatic responses to EMT-inducing signals.

overall_design: mRNA profiles of human oral squamous cell carcinoma cells (CAL27 cell line) with shRNA-mediated QKI knock-down and mock-infected

first: Ji

middle: H

last: Hong

first: Yoon

last: Ko

first: Young-Ho

last: Ahn


title: Next generation sequencing of wild-type and Meis2 otic vesicle transcriptomes

city: Valladolid

first: Thomas

last: Schimmang

address: Sanz y Fores 3

institute: CSIC

summary: We report the RNAseq analysis of otic vesicles isolated from mouse wild-type and Meis2 mutant embryos at embryonic day 11.5 of development.

overall_design: Otic vesicle mRNA profiles of wild-type (WT) and Meis2 mutant mice (KO) were generated by deep sequencing, in duplicate, using Illumina. 18 genes with a FDR <0.05 were detected.

first: Carlos

last: Prieto Sánchez


title: KLF3 mediates epidermal differentiation through the epigenomic writer CBP [RNA-seq]

first: George

last: Sen

overall_design: KLF3 knockdown, KLF4 knockdown, KLF3/KLF4 double knockdown, CBP knockdown, and P300 knockdown RNA-seq in 3 day differentiated primary keratinocytes.

first: Jackson

last: Jones


title: The evolution and functional divergence of the histone H2B family in plants

city: Tübingen

first: Michael

last: Borg

address: Max Planck Ring 5

department: Algal Development & Evolution

institute: Max Planck Insititue for Biology

summary: Chromatin regulation of eukaryotic genomes depends on the formation of nucleosome complexes between histone proteins and DNA. Histone variants, which are diversified by sequence or expression pattern, can profoundly alter chromatin properties. While variants in histone H2A and H3 families are well characterized, the extent of diversification of histone H2B proteins is less understood. Here, we report a systematic analysis of the histone H2B family in plants, which have undergone substantial divergence during the evolution of each major group in the plant kingdom. By characterising Arabidopsis H2Bs, we substantiate this diversification and reveal potential functional specialization that parallels the phylogenetic structure of emergent clades in eudicots. In addition, we identify a new class of highly divergent H2B variants, H2B.S, that specifically accumulate during chromatin compaction of dry seed embryos in multiple species of flowering plants. Our findings thus identify unsuspected diverse properties among histone H2B proteins in plants that has manifested into potentially novel groups of histone variants.

overall_design: Genome-wide maps of somatic H2B deposition in Arabidopsis seedlings


title: LIN28B Regulates Transcription and Potentiates MYCN-induced Neuroblastoma in a let-7-independent Manner [RNA-seq]

city: Hangzhou

first: Ting

last: Tao

state: Zhejiang

address: 3333 Binsheng Road

institute: Children's Hospital, Zhejiang University School of Medicine

summary: LIN28B is highly expressed in neuroblastoma and promotes tumorigenesis at least in part through inhibition of let-7 microRNA biogenesis. Here, we report that overexpression of either wild-type LIN28B, or a LIN28B mutant that is unable to bind and inhibit let-7, accelerates the onset and increases the penetrance of MYCN-induced neuroblastoma, potentiates the invasion and migration of transformed sympathetic neuroblasts and drives the distant metastases in vivo. Genome-wide ChIP-seq analysis and co-immunoprecipitation experiments show that LIN28B indirectly binds active gene promoters in neuroblastoma cells through an interaction with ZNF143 and activates the expression of downstream targets, including GSK3B and L1CAM, which are involved in neuronal cell adhesion and migration. These findings reveal an unexpected, let-7-independent function for LIN28B in transcriptional regulation during neuroblastoma pathogenesis.

overall_design: RNA-Seq for BE2C cells engineered with a doxycycline-inducible overexpression of wild-type or mutant LIN28B, untreated (nDox) or treated (yDox) with doxycycline

last: Shi

first: Luca

last: Mariani

first: Brian

middle: J

last: Abraham

first: Adam

last: Durbin

first: Mark

middle: W

first: John

last: Powers

first: Pavlos

last: Missios

first: Kenneth

middle: N

last: Ross

first: Antonio

last: Perez-Atayde

first: Martha

last: Bulyk

first: Richard

last: Young

middle: Q

last: Daley

first: A

last: Look


title: Alteration of in vivo gene expression in Drosophila intestinal stem cells after OXPHOS disruption and the role of FOXO in it.

city: Bethesda

first: Mehdi

last: Pirooznia

address: 12 SOUTH DR

institute: National Institutes of Health

summary: To investigate the in vivo gene expression changes in Drosophila intestinal stem cells (ISCs) when OXPHOS   is disrupted and the role of FOXO in regulating this process, we dissected midguts from 4 groups of adult flies: "esg-GAL4,tub-GAL80TS,UAS-nlsGFP/UAS-mitoXhoI;UAS-pAbp-FLAG/+ & homoplasmic mt:CoIsyn" (C group), "esg-GAL4,tub-GAL80TS,UAS-nlsGFP/UAS-mitoXhoI;UAS-pAbp-FLAG/+ & heteroplasmic mt:CoIT300I" (H group, also called M group), "esg-GAL4,tub-GAL80TS,UAS-nlsGFP/UAS-mitoXhoI;UAS-pAbp-FLAG/UAS-FOXO-IR & homoplasmic mt:CoIsyn" (FC group), "esg-GAL4,tub-GAL80TS,UAS-nlsGFP/UAS-mitoXhoI;UAS-pAbp-FLAG/UAS-FOXO-IR & heteroplasmic mt:CoIT300I" (FH group, also called FM group), ~200 midguts per group. The flies were initially obtained and maintained at 18 °C till 2 days after eclosion and were then heat-shocked at 37 ºC for 2 hours and maintained in 29 °C for 5 days. Thus, the ISCs of H and FH group flies were carrying the lethal homoplasmic mitoXhoI-resistant mt:CoIT300I mitochondrial DNAs (mtDNAs) with the wild-type mtDNAs eliminated by mitoXhoI and the OXPHOS disrupted. Meanwhile, the ISCs of C and FC group flies were still carrying wild-type-like but mitoXhoI-resistant mt:CoIsyn mtDNAs. Through the mRNA tagging method with the expressed FLAG-tagged poly(A)-binding protein (pAbp) and anti-FLAG affinity pull-down, We purified and compared mRNA transcriptome profiles (RNA-seq) of different ISCs groups in duplicates. We found about 10% of the mRNAs we detected were either up-regulated or down-regulated in the OXPHOS-disrupted (M group) ISCs compared with control (C group). The down-regulated pool included many genes involved in cell differentiation, proliferation, and growth regulation. The up-regulated pool was enriched in genes participating in various metabolic processes, including glycolysis and fatty acids synthesis. This result suggests a possible metabolic adaptation in response to the OXPHOS deficiency in M group ISCs. Importantly, knockdown of FOXO in OXPHOS-disrupted ISCs restored the expression level of more than 50% of the up- or down-regulated genes, indicating that transcriptional response to OXPHOS deficiency is partially mediated by FOXO. We also noticed that genes whose expressions were altered in OXPHOS-disrupted ISCs included many related to Notch signaling, indicating the mis-regulation of this signaling in these ISCs.

overall_design: Total mRNA were extracted from the ISCs of C, M, FC and FM group of flies.   The mRNA profiles were generated in duplicates using Hiseq3000.

first: Fan

last: Zhang

first: Hong

last: Xu


title: Transcriptomic insight into salinomycin mechanisms in breast cancer cell lines: synergistic effects with dasatinib and induction of estrogen receptor beta

city: New York

first: Genomics-core-facility

last: WCM

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

summary:
Purpose:The use of a single-drug to encounter cancer progression is generally ineffective due to the tumors heterogeneity. To improve the clinical outcome, multiple drugs of distinctive mechanisms but complementary anticancer activities (combination therapy) are often used to enhance antitumor efficacy and minimize the risk of acquiring drug resistance. In this study, we proposed to use a combination of salinomycin (which targets anticancer stem cells) and dasatinib (an Src kinase inhibitor) for the treatment of breast cancer. The use of a RNA-seq is a combinatorial technique that allows to quantify global gene expression in biological samples. We employed this next generation sequencing technique to provide an initial insight into how Sal and Das alone, as well as in combination, modulated gene expression in the MDA-MB-468 human triple negative breast cancer cell line.

Method: mRNA profiles of MDA-MB-468 cells treated with PBS (control), salinomycin, dasatinib, or the drug combination Sal + Das were generated by deep sequencing, in quadruplicate, using HiSeq4000 sequencer with single-end 50 bps reads. The results were validated by RT-qPCR analysis using StepOnePlus Real-timePCR system and SYBR Green assays.

Results: RNA-seq data revealed that both salinomycin and dasatinib inhibit the expression of many downstream targeted genes of the STAT3, Wnt/beta-catenin, and hedgehog cell signaling pathways. The drug combination exhibited synergism through suppression of multiple pathways, leading to a promotion of cell cycle arrest at the G1/S phase mainly via the estrogen-mediated S-phase entry pathway, and partially via the BRCA1 and DNA damage response pathway. We also identified new salinomycin mechanisms involved in upregulating transcription factor 2. The study further led to a discovery of a new drug-induced targeting of estrogen receptor beta approach for triple-negative breast cancer treatment.

Conclusion: Using RNA-seq, we identified for the first time the responsible pathways, including the estrogen-mediated S-phase entry pathway, that contributed to the synergistic effects of the drug combination Sal + Das. The discoveries of potential therapeutic targets, such as E2F2 as well as a novel drug-induced targeting of estrogen receptor beta (ESR2) approach were also described herein.We believe that using next generation approach to study drug mechanisms will allow us to identify more specific disease-relevant biomarkers for precision treatment of breast cancer, as well as other cancers in the future.

first: Vanessa

last: Bellat

first: Benedict

last: Law


title: Circulating miRNAs as a predictive biomarkers of progression from prediabetes to diabetes: outcomes of 5-year prospective observational study

city: Bialystok

first: Iwona

last: Sidorkiewicz

address: Sklodowska-Curie Street 24a

department: Clinical Research Centre

country: Poland

institute: Medical University of Bialystok

summary:
The aim of this study was to conduct a baseline comparison of serum-circulating miRNA in prediabetic individuals with the distinction between those who later progressed to type 2 diabetes (T2DM) and those who did not. The expression level of 798 miRNAs using NanoString technology was examined. Spearman correlation, ROC curve analysis, and logistic regression modeling were performed. Gene ontology (GO), canonical pathways analysis were used to explore the biological functions of the miRNA target genes.
The study revealed that 18 miRNAs were upregulated in serum samples of patients who later progressed to T2DM. Pathway analysis showed that miRNA target genes were mainly significantly enriched in neuroinflammation signaling, Myc mediated apoptosis signaling and tumoricidal function of hepatic natural killer (NK) cells. ROC analysis demonstrated that miR-491-5p, miR-1307-3p, and miR-298 can be introduced as a diagnostic tool for the prediction of T2DM (AUC=97.1%; 90.2%; 88.7%; respectively). Validation by qRT-PCR confirmed our findings. The results suggest that circulating miRNAs can potentially be used as predictive biomarkers of T2DM in prediabetic patients.

overall_design: 30 serum samples of prediabetes patiensts were included. T2DM grop patients developed diabetes after 5 years from baseline visit. Control groupdid not develop T2DM.

first: Magdalena

last: Niemira

last: Krętowski


title: MET Inhibition Elicits PGC1α Dependent Metabolic Reprogramming in Glioblastoma

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: By utilizing proteomic and transcriptomic analysis coupled with untargeted polar and non-polar metabolite analysis by liquid chromatography/mass spectrometry, we identified a specific metabolic program elicited by c-MET inhibition. Interference with c-MET drives oxidative metabolism by increasing fatty acid oxidation (FAO) and glucose anaplerosis, which was orchestrated by the master-regulator, PGC1α. Based on a drug screen, we further found that the mitochondrial matrix chaperone inhibitor, gamitrinib, along with c-MET inhibition causes synergistic cell death, which was mechanistically related to the ability of gamitrinib to suppress oxidative metabolism. In alignment with these findings, FAO inhibitor, etomoxir, enhanced the anti-proliferative effects of c-MET inhibition as well. Both combination therapies were active in vivo, suggesting two novel potential combination therapies, involving c-MET inhibitors.

overall_design: GBM14 cells were chronically treated with 1 µM crizotinib for 14 days. Thereafter, cells were harvested and subjected to RNA extraction. RNA was subsequently processed for microarray analysis.

first: Thi

last: Nguyen

first: Markus

last: Siegelin